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HGVS > Self ass Q&A > Flashcards

Self ass Q&A Flashcards

1
Q

BJ, a technologist, comes to Dr. Z, the director of a
clinical pathology laboratory, with a question
about the nomenclature of genomic variants. This
is the first time that BJ has worked on reviewing
wet laboratory results and writing nomenclature.
Dr. Z explains to BJ what “c.,” “g.,” “m.,” “n.,”
“r.,” and “p.” stand for in nomenclature, with
examples. One of examples is myoclonic epilepsy
with ragged red fibers (MERRF). Which one of the
following nomenclatures may be used to describe a
functional, effective variant for MERRF?
A. c.8344A>G
B. g.8344A>G
C. m.8344A>G
D. n.8344A>G
E. r.8344A >G
F. p.8344A>G
G. None of the above

A

C. m.8344A>G

Myoclonic Epilepsy with Ragged Red Fibers syndrome is a mitochondrial di

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2
Q

John was evaluated for the genetic etiology of his
recurrent respiratory infection and
cardiomyopathy when he was 18 months old. His
developmental milestones were normal. Family
history indicated an X-linked recessive trait. Barth
syndrome was at the top of the list of differential
diagnoses. Sanger sequencing of the TAZ gene on
Xq28 for Barth syndrome was ordered. A C-to-G
transversion in exon 5 was detected in John’s
peripheral-blood sample, which was a nonsense
mutation. Which one of the following
nomenclatures may be used to describe this
functional, effective variant?
A. c.153C . G
B. g.153C . G
C. m.153C . G
D. n.153C . G
E. r.153C . G
F. p.153C . G
G. None of the above

A

A. c.153C>G

Mutations in the TAZ gene cause Barth syndrome.

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3
Q

Dr. Z, a director of a clinical pathology laboratory,
reviewed a patient’s Sanger sequencing results on
USH1A for Usher syndrome. By sequencing only
the exons and 20-bp introns on either side of the
exons, one variant of unknown clinical significance
(VUCS) was found, which changed an aspartic
acid (Asp/D) into tyrosine (Tyr/Y). Which one of the nomenclatures may Dr. Z use to describe this
variant at the DNA level?
A. a.1268C . T
B. c.1268C . T
C. g.1268C . T
D. p.1268C . T
E. All of the above
F. None of the above

A

B. c.1268C>T

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4
Q

Dr. Z, a director of a clinical pathology laboratory,
reviewed a patient’s Sanger sequencing results on
USH1A for Usher syndrome. By sequencing only
the exons and 20-bp introns on either side of the
exons, one variant of unknown clinical significance
(VUCS) was found, which changed an aspartic
acid (Asp/D) into tyrosine (Tyr/Y). Which one of
the nomenclatures may Dr. Z use to describe this
variant at the amino acid level?
A. a.D401Y
B. c.D401Y
C. g.D401Y
D. p.D401Y
E. All of the above
F. None of the above

A

D. p.D401Y

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5
Q

Which one of the following nomenclatures should
be used to describe ACTTTGTGCC to ACTTTGTGGCC?
A. c.8dupG
B. c.8Gdup
C. c.8_9insG
D. c.8_9Gins
E. None of the above

A

A. c.8dupG

duplicating insertions are described as duplications, not as insertions

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6
Q

Autosomal recessive nonsyndromic hearing loss
and deafness (DFNB1) is characterized by
congenital, nonprogressive, mild to profound
sensorineural hearing impairment. The majority of
individuals with DFNB1 have two identifiable
variants in the GJB2 gene, but some have
compound heterozygous variants of the GJB2 and
GJB6 genes. If an individual has a maternally
inherited c.35delG in GJB2 and a paternally
inherited c.14C>T in GJB6, which one of the
following nomenclatures would be appropriate to
use in the molecular report?

A. GJB2:c.35delG;GJB6:c.14C>T
B. GJB2:c.[35delG];GJB6:c.[14C>T]
C. GJB6:c.14C>T;GJB2:c.35delG
D. GJB6:c.[14C>T];GJB2:c.[35delG]
E. A and C
F. B and D
G. None of the above

A

F. B and D

descriptions of sequence changes in different genes (e.g., for recessive diseases) are listed between square brackets, separated by a semicolon and include a reference to the sequence (gene) changed; DMD:c.[76A>C];GJB:c.[87delG] There is no requirement with regard to the order of the two genes.

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7
Q

Which one of the following nomenclatures is
appropriate, according to published
nomenclature for the description of sequence variants by the Human Genome Variation Society in 2016?

A. c.IVS2 + 2T>G
B. LRG_1:g.8463-2G>C
C. c.88+2U>G
D. c.* 46T>A
E. All of the above
F. None of the above

A

c.* 46T >A

c.* 46T >A denotes a T-to-A substitution 46 nucleotides 30 prime of the translation
termination codon

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8
Q

Which one of the following nomenclatures may be
used to describe a start codon, methionine
(Met, M), is changed to valine (Val, V), which
activates an upstream translation initiation site
at position -12?
A. p.-12Met
B. p.-12Met1
C. p.-12Met1Val
D. p.Met1Valext-12
E. None of the above

A

D. p.Met1Valext-12
or
p.Met1ext-12

to describe an amino acid Met1 is changed to Val activating an upstream translation initiation site at position -12
(methionine-12).

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9
Q

Which one of the following nomenclatures may be
used to describe a variant in the stop codon at
position 110 of an amino acid sequence, changing
it to a codon for glutamine (Gln, Q) and adding a
tail of 17 new amino acids (including Gln/Q) to
the protein’s C-terminus ending at a new stop
codon?

A. p.110Glnext17
B. p.Ter110Glnext17
C. p.Ter110Gln
D. p.110GlnextTer17
E. p.*110Gln

A

A. p.* 110Glnext* 17
or
p.Ter110GlnextTer17
or
p.* 110Qext* 17

a change affecting the translation termination codon (Ter/* ) introducing a new downstream termination codon extending the C-terminus of the encoded protein described using “extTer#” (alternatively “ext* #”), where “#”
is the position of the new stop codon (Ter#/* #).

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10
Q

Which one of the following nomenclatures may be
used to describe a chimeric organism in which a
chromosome in some cells contains a normal
sequence (arginine, Arg/R) at position 83, while
other cells contain another chromosome with
serine (Ser/S) at this position?

A. p.[Arg83=/Arg83Ser]
B. p.[Arg83=//Arg83Ser]
C. p.[Arg83=];[Arg83Ser]
D. p.[Arg83=;Arg83Ser]
E. p.[Arg83=(;)Arg83Ser]
F. None of the above

A

B. p.[Arg83=//Arg83Ser]

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11
Q

Which one of the following nomenclatures may be
used to describe a somatic mosaic case in which a
chromosome in some cells contains a normal
sequence (arginine, Arg/R) at position 83, while
other cells contain a serine (Ser/S) at this position?

A. p.[Arg83 = /Arg83Ser]
B. p.[Arg83 = //Arg83Ser]
C. p.[Arg83 = ];[Arg83Ser]
D. p.[Arg83 = ;Arg83Ser]
E. p.[Arg83 = (;)Arg83Ser]
F. None of the above

A

A. p.[Arg83 = /Arg83Ser]

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12
Q

Which one of the following nomenclatures may be
used to describe two changes (amino acid alanine
changes threonine at the position 25 and proline to
leucine at the position 323, RNA or protein
analyzed) were identified in one individual, but it
is not known whether these changes are on the
same chromosome (in cis) or on different
chromosomes (in trans)?

A. p.[Arg83 = /Arg83Ser]
B. p.[Arg83 = //Arg83Ser]
C. p.[Arg83 = ];[Arg83Ser]
D. p.[Arg83 = ;Arg83Ser]
E. p.[Arg83 = (;)Arg83Ser]
F. None of the above

A

E. p.[Arg83 = (;)Arg83Ser]

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13
Q

Which one of the following nomenclatures
may be used to describe a homozygous
A-to-C change at the nucleotide position 76
of a cDNA?

A. c.[76A>C];[76A>C]
B. c.[76A>C];[(76A>C)]
C. c.[76A>C];[ = ]
D. c.[76A>C];[0]
E. None of the above

A

A. c.[76A>C];[76A>C]

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14
Q

Which one of the following nomenclatures may be
used to describe a heterozygous A-to-C change at
the nucleotide position 76 of a cDNA?

A. c.[76A>C];[76A>C]
B. c.[76A>C];[(76A>C)]
C. c.[76A>C];[ = ]
D. c.[76A>C];[0]
E. None of the above

A

D. c.[76A>C];[0]

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15
Q

Which one of the following nomenclatures may be
used to describe a chimeric case in which at position
83, in addition to the normal sequence (a G), some
cells are found containing another chromosome
containing a C at this position?

A. c.[83G = /83G>C]
B. c.[ = /83G>C]
C. c.[83G = //83G>C]
D. c.[ = //83G>C]
E. None of the above

A

C. c.[83G = //83G>C] or D in the book

check the ans

The ans to this Q maybe wrong in the book

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16
Q

Which one of the following nomenclatures may be
used to describe a mosaic case in which at
position 83, in addition to the normal
sequence (a G), chromosomes are also found
containing a C?

A. c.[83G = /83G>C]
B. c.[ = /83G>C]
C. c.[83G = //83G>C]
D. c.[ = //83G>C]
E. None of the above

A

A. c.[83G = /83G>C]

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17
Q

Which one of the following nomenclatures
is appropriate according to recommendations
for the description of sequence variants
published by the Human Genome Variation
Society in 2016?

A. m.[76u>c]
B. m.[ = ,73_88del]
C. r.[76t>c]
D. r.[= ,73_88del]
E. None of the above

A

D. r.[= ,73_88del]

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18
Q

Which one of the following nomenclatures is appropriate, according to recommendations for the description of RNA sequence variants published by the Human Genome Variation
Society in 2016?

A. r.[88G >A]
B. r.[ = ,73_88del]
C. r.[76T>C]
D. r.[76t>c,73_88del]

A

B. r.[ = ,73_88del]

“r.” is used to indicate
that a change is described at the RNA level, and
nucleotides are designated by the bases (in lower
case). T (tyrosine) is one of the bases for DNA,
which is replaced by u (uracil) at the RNA level. therefore other options are wrong

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19
Q

A reference sequence ATG GCC AAT is
mutated to … cag ATG TCC AAT CTT GCT
AGC CCT AGA TTT GGT TCT … in a
sample. Which one of the following
nomenclatures is the most appropriate one to describe this change?

A

B. c.4G>T(p.Ala2Ser)

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20
Q

A reference sequence ATG GCC AAT is
mutated to … cag ATG TCC AAT CTT GCT AGC
CCT AGA TTT GGT TCT … in a sample.
Which one of the following nomenclatures
is the most appropriate one to describe this
change?

A

C. c.4G>T(p.Ala2Ser)

similar to above Q

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21
Q

A reference sequence ATG GCC AAT is
mutated to … cag ATG TGC AAT CTT GCT
AGC CCT AGA TTT GGT TCT … in a
sample. Which one of the following
nomenclatures is the most appropriate one to
describe this change?

A

C. c.4_5delinsTG(p.Ala2Cys)

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22
Q

A reference sequence …cag ATG GCC in is
mutated to … ttg ATG GCC AAT CTT GCT
AGC CCT AGA TTT GGT TCT … in a
sample. Which one of the following
nomenclatures is the most appropriate one to
describe this change?

A

c.-3-2delinsTT
or
c.-3-2delCAinsTT

intronic affecting splice site

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23
Q

A reference sequence TTT GGT TCT cca …is mutated
to … cag ATG GCC AAT CTT GCT AGC CCT
AGA TTT GGT TCT ctt … in a sample. Which one
of the following nomenclatures is the most
appropriate one to describe this change?

A

c.33+2_ +3delinsTT

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24
Q

A reference sequence TTT GGT TCT cca … is mutated
to … cag ATG GCC AAT CTT GCT AGC CCT
AGA TTT GGT TCT ctt … in a sample. Which one
of the following nomenclatures is the most
appropriate one to describe this change?

A

c.33+2_ +3delinsTT
or
c.[33+2C >T;33+3A>T]

second format is not prefered

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25
Q

A reference sequence …cag GGA GCC AAT is mutated
to … aag GGA GCC AAT CTT GCT AGC CCT
CAT AGA TTT GGT TCT cat… in a sample.
Which one of the following nomenclatures
is the most appropriate one to describe this
change?

A

c.76-3G>A

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26
Q

A reference sequence … cag GGA GCC AAT is mutated
to … caa GGA GCC AAT CTT GCT AGC CCT
AGA TTT GGT TCT. Which one of the following
nomenclatures is the most appropriate one to
describe this change?

A

c.76-1G>A

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27
Q

A reference sequence TTT GGT TCT gtt … tag GAC is
mutated to … cag GGA GCC AAT CTT GCT
AGC CCT AGA TTT GGT TCT gct … tag GAC in
a sample. Which one of the following
nomenclatures is the most appropriate one to
describe this change?

A

c.108+2T>C

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28
Q

A reference sequence …cag GGA GCC AAT is
mutated to … cag TGA GCC AAT CTT GCT AGC
CCT AGA TTT GGT TCT gtt … tag GAC in a
sample. Which one of the following nomenclatures
is the most appropriate one to describe this
change?

A

c.76G>T(p.G26*)

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29
Q

A reference sequence … cag GGA GCC AAT is
mutated to … cag TGA GCC AAT CTT GCT AGC
CCT AGA TTT GGT TCT gtt … tag GAC in a
sample. Which one of the following nomenclatures
is the most appropriate one to describe this
change?

A

c.76G>T(p.Gly26*)
or
c.76G>T(p.Gly26Ter)

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30
Q

A reference sequence TTT GGT TAG gtt … is mutated
to … cag GGA GCC AAT CTT GCT AGC CCT
AGA TTT GGT TAG ttt … in a sample.
Which one of the following nomenclatures
is the most appropriate one to describe this
change?

TAG is a stop codon

A

c.*1G>T

TAG, TAA, and TGA are stop codons.

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31
Q

A reference sequence TTT GGT TAG gtt …is mutated
to … cag GGA GCC AAT CTT GCT AGC CCT
AGA TTT GGT TAT gtt … in a sample. Which one
of the following nomenclatures is the most
appropriate one to describe this change?

A

c.365G>T(p.Ter121TyrextTer22)
or
c.365G>T(p.121Tyrext22)

stop codon replaced by tyrosin, this change affecting translation termination and described as extentsion

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32
Q

reference sequence TTT GGT TAG gtt …is mutated
to … cag GGA GCC AAT CTT GCT AGC CCT
AGA TTT GGT TAT gtt … in a sample. Which one
of the following nomenclatures is the most
appropriate one to describe this change?

A

c.365G>T(p.Ter121TyrextTer22)
or
c.365G>T(p.121Tyrext22)

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33
Q

reference sequence TTT GGT TAG gtt …is mutated
to … cag GGA GCC AAT CTT GCT AGC CCT
AGA TTT GGT TAA gtt … in a sample. Which one
of the following nomenclatures is the most
appropriate one to describe this change?

A

c.365G>A(p.Ter121=)

one termination codon is changinf to another one

TAG, TAA, and TGA are stop codons.

34
Q

reference sequence TTT GGT TAG gtt …is mutated
to … cag GGA GCC AAT CTT GCT AGC CCT
AGA TTT GGT TGA gtt … in a sample. Which one
of the following nomenclatures is the most
appropriate one to describe this change?**

A

c.364_365delinsGA(p.*121=)

wrong c. in the book

35
Q

A reference sequence … cag ATG GCC AAT is mutated
to … cag TTG GCC AAT CTT GCT AGC CCT
AGA TTT GGT TCT … in a sample. Which one of
the following nomenclatures is appropriate to
describe this change?

A

c.1A>T(p.Met1ext-5)
or
c.1A>T(p.Met1Leuext-5)

A change affecting the translation initiation codon (Met-1) introduces a new upstream initiation codon extending the N-terminus of the encoded protein described using “ext-#,” where “-#” is the position of the new initiation codon (Met-#).

36
Q

A reference sequence … cag ATG GCC AAT is mutated
to … cag TTG GCC AAT CTT GCT AGC CCT
AGA TTT GGT TCT … in a sample. Which one of
the following nomenclatures is appropriate to
describe this change?

A

c.1A >T(p.M1Lext-5)

same Q as 35 different way of writting it

37
Q

A reference sequence CTT GCT AGC CCT is mutated
to … cag GGA GCC AAT CTT GC AGC CCT
AGA TTT GGT TCG gtt … tag GAC in a sample.
Which one of the following nomenclatures is the
most appropriate one to describe this change?

A

c.90del(p.A30fs)

38
Q

A reference sequence AAT CTT GCT AGC CCT is mutated
to … cag GGA GCC AAT CTT G AGC CCT AGA
TTT GGT TCG gtt … tag GAC in a sample. Which
one of the following nomenclatures is the most
appropriate one to describe this change?

A

c.89_90del(p.A30fs)
or
c.89_90delCT(p.Ala30GlufsTer3)

TAA, TAG, and TGA are the stop codons.

There is a 2-bp deletion at exon 3 of a gene in the question, which causes a frameshift change at the position 30 of amino acid sequence from alanine to glutamic acid. After the change, the third codon is TAG, a stop codon.

39
Q

A reference sequence AAT CTT GCT AGC CCT AGA is mutated
to … cag GGA GCC AAT CTT G GC CCT AGA
TTT GGT TCG gtt … tag GAC in a sample. Which
one of the following nomenclatures is the most
appropriate one to describe this change?

A

c.89_91del(p.A30_S31delinsG)
or c.89_91delCTA(p.Ala30_Ser31delinsGly)

40
Q

A reference sequence TTT GGT TCG gtt … tag GAC is mutated
to … cag GGA GCC AAT CTT GCT AGC CCT
AGA TTT GGT TC gtt … tag GAC in a sample.
RNA analysis shows no effect on splicing. Which
one of the following nomenclatures is the most
appropriate one to describe this change?**

A

c.108del(p.S36fs)
or
c.108delG(p.Ser36fs)

41
Q

A reference sequence GGT TCG gtt … tag is
mutated to … cag GGA GCC AAT CTT GCT
AGC CCT AGA TTT GGT TC gtt … tag GAC in a sample. RNA analysis shows effect on
splicing. Which one of the following
nomenclatures is the most appropriate one to describe this change?

A

c.108+1delG

since the RNA analysis showed splicing affect, the G deleted is from intron so we have TCG .tt

42
Q

A reference sequence CTT GCT AGC CCT is mutated to … cag GGA GCC AAT CTT GCT GGA AGC CCT AGA TTT GGT TCG gtt … tag GAC in a sample. Which one of the following nomenclatures is the most appropriate one to describe this
change?

A

c.90_91insGGA (p.A30_S31insG)

a 3-bp insertion in the question,
which adds a glycine between alanine at position
30 and serine at position 31. This is an in-frame
change

43
Q

A reference sequence CTT GCT AGC is mutated
to … cag GGA GCC AAT CTT GCGGAT AGC
CCT AGA TTT GGT TCG gtt … tag GAC in a
sample. Which one of the following nomenclatures
is the most appropriate one to describe this
change?

A

c.89_90insGGA (p.Ala30delinsAlaGly).

44
Q

A reference sequence CTT GCT AGC CCT is mutated
to … cag GGA GCC AAT CTT GGA GCC CCT
AGA TTT GGT TCG gtt … tag GAC in a sample.
Which one of the following nomenclatures is the
most appropriate one to describe this change?

A

c.88_93delinsGGAGCC(p.A30_S31delinsGA) or
c.88_93delinsGGAGCC(p.Ala30_Ser31delinsGlyAla)

45
Q

A reference sequence CTT GCT AGC is mutated
to … cag GGA GCC AAT CTT GCAGCC AGC
CCT AGA TTT GGT TCG gtt … tag GAC in a
sample. Which one of the following nomenclatures
is the most appropriate one to describe this
change?

A

c.90delinsAGCC(p.Ala30delinsAlaAla)

46
Q

A reference sequence GCT AGC AGC AGC TTT (the last AGC are 22, 23, 24) is mutated
to … cag ATG GCC AAT CTT GCT AGC AGC
TTT GGT TCT … in a sample. ACG in exon 1 of
this gene is not a common polymorphism in the
general population. Which one of the following
nomenclatures is right to describe this change?

A

c.22_24del(p.Ser8del)

There is a 3-bp deletion in the question, which deletes one of the three serines. This is an in-frame change

47
Q

A reference sequence GCT AGC AGC CGA is mutated
to … cag ATG GCC AAT CTT GCT AGC AGC AGC CGA TTT GGT TCT… in a sample. The
variant is not a common polymorphism in the
general population. Which one of the following
nomenclatures is right to describe this change?

A

c.19_21dupAGC(p.Ser7dup)

48
Q

A reference sequence TCG gtt gac is mutated
to … cag GGA GCC AAT CTT GCT AGC CCT
AGA TTT GGT TCG gttt gac … in a sample. The
variant is not a common polymorphism in the
general population. Which one of the following
nomenclatures is the most appropriate one to
describe this change?

A

c.108+3dupT

There is a single base-pair insertion/duplication
at intron 4

49
Q

A reference sequence ATG GCC AAT CTT is mutated
to … cag ATG TAA CCG CTT GCT AGC CCT
AGA TTT GGT TCT… in a sample. Which one of
the following nomenclatures is correct to describe
this change?

A

c.4_9inv(p.Ala2_Asn3delinsTer)

The inversion of the six base pairs in the exon 1 of this
gene causes a nonsense variant at position 2 of the
amino acid sequence.

50
Q

A reference sequence ATG GCC AAT is mutated to … cag ATG GCC GCC AAT CTT GCT AGC
CCT AGA TTT GGT TCT … in a sample. Which
one of the following nomenclatures is correct to
describe this change?

A

c.4_6dupGCC(p.Ala2dup)

51
Q

A reference sequence …cag ATG GCC AAT CTT is mutated
to … cag ATG AAT CTT GCT AGC CCT AGA
TTT GGT TCT … in a sample. Which one of the
following nomenclatures is correct to describe this
change?

A

c.4_6del(p.Ala2del)

52
Q

A reference sequence … cag ATG GCC AAT CTT GCT is mutated to … cag ATG GCC AT CTT GCT AGC CCT AGA
TTT GGT TCT … in a sample. Which one of the
following nomenclatures is right to describe this
change?

A

c.8del(p.Asn3fs)
or
c.8delT(p.Asn3IlefsTer26)

53
Q

A reference sequence GGT TCT gtt tta… is mutated to … cag GGA GCC AAT CTT GCT AGC CCT AGA TTT GGT TCT gtt ta… in a sample. The
variant is not a common polymorphism in the
general population. Which one of the following
nomenclatures is the most appropriate one to
describe this change?

A

c.365+5del

the most 3prime, For example, ctttagGCATG to cttagGCATG in an
intron is described as c.301-3delT (not as c.301-
5delT).

54
Q

A reference sequence GGT TCT gtg tga cat… is mutated
to … cag GGA GCC AAT CTT GCT AGC CCT
AGA TTT GGT TCT gtg tc cat … in a sample.
Which one of the following nomenclatures is NOT
appropriate to describe this change?

A

c.365+5_365+6delinsC
or
c.365+5_365+6delGAinsC

ga is replaced by c

55
Q

A reference sequence GGT TCT gtc tca cat … is mutated to … cag GGA GCC AAT CTT GCT AGC CCT AGA TTT GGT TCT gtc tct ctc aca t … in a sample. The TC repeat in intron 11 of this gene is
polymorphic in the general population. Which one
of the following nomenclatures is appropriate to
describe this change?

A

c.365+2+3[4]
or
c.365+4+5[4]
or
c.365+2TC[4]

NOTE: polymorphisms are different from duplication,don’t use dup for pol

There are extra two copies of TC repeats in intron 11 of this gene. So the total number of the TC repeat after the change is 4. In the question, it mentioned that this TC repeat is polymorphic in the general population. It may not change the amino acid sequence. for example ” Forexample, g.7_8[4] (or g.5_6[4], or g.5TG[4], not
g.7_10dup)

56
Q

A reference sequence GGT TCT gtc tca cat … is mutated
to … cag GGA GCC AAT CTT GCT AGC CCT
AGA TTT GGT TCT gtc tct ctc aca t … in a
sample. The TC repeat in intron 11 of this gene is
polymorphic in the general population. Which one
of the following nomenclatures is the most
appropriate one to describe this change?

A

c.365+2TC[4]

polymorphism therefore **don’t **use ins

There are extra two copies of TC repeats in the intron 11 of this gene. So the total number of the TC repeat is 4 after the change. I

57
Q

A reference sequence GGT TCT gtc tca cat … is mutated to … cag GGA GCC AAT CTT GCT AGC CCT
AGA TTT GGT TCT g**tc tct ctc **aca t … in a
sample. The TC repeat in intron 11 of this gene is
polymorphic in the general population. Which one
of the following nomenclatures is the most
appropriate one to describe this change?

A

c.365+2+3[4]
or
c.365+4+5[4]
or
c.365+2TG[4]

if you do +2_+3 no need to mention TC but if you do only +2 for example mention the repeat

58
Q

A reference sequence TCT gtc tca cat … is mutated
to … cag GGA GCC AAT CTT GCT AGC CCT
AGA TTT GGT TCT gtc tct ctc aca t … in a
sample. The TG repeat in intron 11 of this gene is
polymorphic in the general population. Which one
of the following nomenclatures is the most
appropriate one to describe this change?

A

c.365+2TC[4]
or
c.365+2+3[4]
or
c.365+4+5[4]

59
Q

A technologist analyzed a peripheral-blood
sample with an assay for hereditary
hemochromatosis in a clinical molecular genetic laboratory. The patient had a C282Y and a H63D mutation in the HFE gene. Parental tests confirmed that the C282Y was from the mother, while H63D was from the father. Which one of the following nomenclatures is the most
appropriate one for this patient?

A

p.[H63D];[C282Y]

compound hetrozygous

60
Q

A technologist analyzed a peripheral-blood sample with an assay for hereditary hemochromatosis in a clinical molecular genetic laboratory. The patient
had a C282Y and a H63D mutation in the HFE gene. Parental tests have not been done. Which one of the following nomenclatures is the most
appropriate one for this patient?

A

p.[H63D(;)C282Y]

61
Q

A technologist analyzed a peripheral-blood sample with an assay for hereditary hemochromatosis in a clinical molecular genetic laboratory. The patient
had a C282Y and a H63D mutation in the HFE gene. Parental tests confirmed that both C282Y and H63D were maternal in origin. Which one of the
following nomenclatures is the most appropriate one for this patient?

A

p.[H63D;C282Y]

62
Q

Fragile X molecular testing was ordered for a 4- year-old boy with mental retardation. PCR and Southern blot methods were used for the analysis, and they detected one methylated allele with approximately 1000 CGG repeats. Which one of the
following nomenclatures is the most appropriate to describe this change?

A

c.-129CGG(1000)

63
Q

A cystic fibrosis (CF) mutation panel was
performed on a pregnant woman. The results showed an R117H mutation with a 5T allele. The parental tests confirmed that both of the variants were maternal in origin. Which one of the following nomenclatures is the most appropriate one to describe these changes?

A

c.[350G>A;1210-12T[5]]

64
Q

A cystic fibrosis (CF) mutation panel was
performed on a pregnant woman. The results showed an R117H mutation with a 5T allele. The parental tests confirmed that R117H was maternal in origin while 5T was paternal in origin. Which one of the following nomenclatures is the most
appropriate one to describe these changes?

A

c.[350G>A];[1210-12T[5]]

65
Q

A cystic fibrosis (CF) mutation panel was
performed on a pregnant woman. The results showed an R117H mutation with a 5T allele. The parental tests have not been done. Which one of the following nomenclatures is the most appropriate one to describe these changes?

A

c.[350G>A(;)[1210-12T[5]]

66
Q

A cystic fibrosis (CF) mutation panel was
performed on a pregnant woman. The results showed a homozygous deltaF508 mutation. The parental tests have not been done. Which one of the following nomenclatures is the most appropriate one to describe this change?

learn
c.[76A>C];[76A>C] denotes a homozygous A to-C change at nucleotide 76.

c.[76A>C];[ = ] denotes a A-to-C change at nucleotide 76 in a gene on one chromosome and a normal coding DNA
reference sequence of the other chromosome.

c.[76A>C];[0] denotes a A-to-C change at
nucleotide 76 in a gene on one chromosome and the absence of the entire coding DNA reference sequence on the other chromosome.

A

c.[1521_1523delCTT];
[(1521_1523delCTT)]

note the parntesees on the second allele

The parental tests have not been done. So it is not
clear if it is a true homozygous change, or a nonamplification of the sequences analyzed on the
other chromosome.

67
Q

A cystic fibrosis (CF) mutation panel was
performed on a pregnant woman. The results showed a heterozygous deltaF508 mutation. Which one of the following nomenclatures is the most appropriate one to describe this change?

A

c.[1521_1523delCTT];[ =]

68
Q

A reference sequence GGT TAG gtt tga gca is mutated to … cag GGA GCC AAT CTT GCT AGC CCT AGA TTT GGT TCG gtt tga gca … in a sample. Which one of the following nomenclatures is the most appropriate one to describe this change?

A

c.364A>C(p.121Serext3)
c.364A>C (p.Ter121SerextTer3)
c.364A>C(p.121Sext3)

stoploss

69
Q

A reference sequence … cag ATG GCC AAT CTT GCT is mutated to … cag ATG CTT GCT AGC CCT AGA CCT
AGA TTT GGT TCT … in a sample. Which one of the following nomenclatures is the most
appropriate one to describe this change?

A

c.4_9del(p.Ala2_Asn3del)

70
Q

A reference sequence … cag ATG GCC AAT CTT GCT is mutated
to … cag ATG GCC AAT GCC AAT CTT GCT AGC CCT AGA TTT GGT TCT … in a sample.
Which one of the following nomenclatures is the most appropriate one to describe this change?

A

c.4_9dup(p.Ala2_Asn3dup)

71
Q

A reference sequence … cag ATG GCC AAT CTT is mutated to … cag ATG GCC AGT GGG AAT CTT GCT AGC CCT AGA TTT GGT TCT … in a sample. Which one of the following nomenclatures is the
most appropriate one to describe this change?

A

c.6_7insAGTGGG(p.Ala2_Asn3insSerGly)

72
Q

A reference sequence … cag ATG GCC AAT CTT is mutated to … cag ATG CGA CTT GCT AGC CCT AGA TTT GGT TCT … in a sample. Which one of the following nomenclatures is the most appropriate one to describe this change?

A

c.4_9delinsCGA(p.Ala2_Asn3delinsArg)

73
Q

The chromatograph below shows sequence results of both directions with a peripheral-blood sample from a 6-year-old girl. A C in the reference sequence of a cDNA is mutated to a T at position 268 in a sample from the patient. Which one of the
following nomenclatures is the most appropriate one?

A

c.[268C>T];[=]

heterozygous change

74
Q

The chromatographs below shows sequence results of exon 6 and exon 8 of a gene from both directions with a peripheral-blood sample from a 6-year-old girl. A C in the reference sequence of a
cDNA is mutated to a T at position 268 in exon 6, and a C to a T at position 343 in exon 12. The targeted parental tests on these two mutations were pending. Which one of the following nomenclatures is the most appropriate one for this
patient?

A

c.[268C>T(;)343C>T]

compound heterozygous variants. The parental tests are pending. So it is not clear whether the two variants are in cis (on the same chromosome) or in trans (on the two homologous chromosomes).

75
Q

The chromatograph below shows sequence
results of both directions with a peripheralblood sample from a 6-year-old girl. A C in the reference sequence of a cDNA is mutated to a T at position 268 in a sample from the patient. The targeted parental tests on this mutation were pending. Which one of the following nomenclatures is the most appropriate
one?

A

c.[268C>T];[(268C>T)]

Homozygous change, note the parantesese on the second allele

76
Q

A 6-year-old boy was brought to a genetics clinic for developmental delay, intellectual disability, and hypotonia. His karyotype and chromosome microarray results are normal. A gene on chromosome X is suspected to be associated with
his symptoms. The chromatograph below shows sequence results of exon 12 in both directions with a peripheral-blood sample from this patient. A C in the reference sequence of a cDNA is mutated to
a T at position 268 in a sample from the patient. The targeted parental tests on this mutation were pending. Which one of the following nomenclatures is the most appropriate one?

A

c.[268C>T];[0]

The male patient has a hemizygous variant in a
gene on chromosome X by chromatograph.

77
Q

A reference sequence … cag GGA GCC GCA GCT GCT AGC is mutated to … cag GGA GCC GCA GCT AGC CCT AGA TTT GGT TCT gtt tta … in a sample. Which one of the following nomenclatures is the most appropriate one to describe this change?

A

c.345_347del(p.Ala115del)

78
Q

A reference sequence GCG GCT AGC is mutated to … cag GGA GCC GCA GCG GCT GCT AGC CCT AGA TTT GGT TCT gtt tta … in a sample. Which one of the following nomenclatures is the most appropriate one to describe this change?

A

c.345_347dup(p.Ala115dup)
or
c.345dupGCT(p.Ala115dup)

79
Q

A reference sequence … cag ATG GCC is mutated to … caa ATG GCC AAT CTT GCT AGC CCT AGA TTT GGT TCT … in a sample. Which one of the following nomenclatures is the most appropriate one to describe this change?

A

c.-1G>A

80
Q

A reference sequence GGT TAG gtt tga gca …is the last exon of a gene, which is mutated to … cag GGA GCC AAT CTT GCT AGC CCT AGA TTT GGT TAG att tga gca… in a sample. Which one of the following nomenclatures is the most appropriate one to describe this change?

A

c.*1G>A

HGVS (2 decks)

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