Brainscape's Knowledge GenomeTM

Browse over 1 million classes created by top students, professors, publishers, and experts.


See full index

HGVS > DNA > Flashcards

DNA Flashcards

1
Q

a substitution of the C nucleotide at g.33038255 by an A

A

NC_000023.10:g.33038255C>A

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
2
Q

a substitution of the G nucleotide at c.93+1 (coding DNA reference sequence) by a T

A

NG_012232.1(NM_004006.2):c.93+1G>T

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
3
Q

nucleotides c.79 and c.80 are replaced by TT

A

LRG_199t1:c.79_80delinsTT

NOTE: changes involving two or more consecutive nucleotides are described as deletion-insertion (delins) so the description c.[79G>T;80C>T] is not correct
NOTE: based on the definition of a substitution, i.e. one nucleotide replaced by one other nucleotide, this change can not be described as a substitution like c.79_80GC>TT or c.79GC>TT

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
4
Q

two substitutions replacing codon CGC (position c.145 to c.147) by TGG

A

NM_004006.2:c.145_147delinsTGG

NOTE: two variants separated by one nucleotide, together affecting one amino acid, should be described as a “delins” so the description c.[145C>T;147C>G] is not correct

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
5
Q

a substitution of the G nucleotide at c.54 (coding DNA reference sequence) by A, C or T (IUPAC code “H”

A

LRG_199t1:c.54G>H

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
6
Q

a screen was performed showing that nucleotide c.123 was a “C” as in the coding DNA reference sequence (the nucleotide was not changed).

A

NM_004006.2:c.123=

NOTE: the description NM_004006.2:c.= can not be used, c.= indicates the entire NM_004006.2 coding DNA reference sequence was analysed and no change was identified.
NOTE: the description LRG_199t1:c.94-23_188+33= indicates no variants where found in the region indicated (exon 3 of the DMD gene).

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
7
Q

a mosaic case where at position 85 besides the normal sequence (a T, described as “=”) also chromosomes are found containing a C (c.85T>C)

A

LRG_199t1:c.85=/T>C

NOTE: irrespective of the frequency in which each nucleotide was found, the reference is always described first

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
8
Q

a chimeric case, i.e. the sample is a mix of cells containing c.85= and c.85T>C.

A

NM_004006.2:c.85=//T>C

NOTE: irrespective of the frequency in which each nucleotide was found, the reference is always described first

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
9
Q

When I only sequenced RNA (cDNA) and not genomic DNA should I then give the description of a variant at DNA level in parenthesis?

A

Yes, while the variant at RNA level can be described as r.76a>g on DNA level, based on e.g. a coding DNA reference, sequence it should be described as c.(76A>G).

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
10
Q

How should I describe a variant in the promoter region of a gene?

A

It is recommended to describe variants in the promoter region of a gene based on a genomic reference sequence, e.g. NC_000023.10:g.33357783G>A (chrX, hg19). Describing the variant in relation to a coding DNA reference sequence (for this variant NM_004006.1:c.-128354C>T or NM_000109.3:c.-401C>T) is possible but not really very informative; you do not know how long the 5’UTR is. The variant can also be described using a genomic reference sequence containing the promoter region (for this variant e.g. L01538.1:g.1407C>T), but again this is not really informative. Although NC_000023.10:g.33357783G>A seems complex, it can be used in a genome browsers helping you to quickly zoom in on the region of interest.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
11
Q

Are polymorphisms described like NM_004006.1:c.76A/G?

A

No, all substitutions are described as NM_004006.1:c.76A>G. In the past, the format c.76A/G has been used to describe “polymorphic” sequence variants. Note that a description should be neutral, simply describe the change, and not include any other information like predicted or known functional consequences.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
12
Q

Can I describe a GC to TG variant as a dinucleotide substitution (NG_012232.1:g.12GC>TG)?

A

No, this is not allowed. By definition a substitution changes one nucleotide into one other nucleotide. The change GAAGCCAG to GAATGCAG should be described as NG_012232.1:g.12_13delinsTG, i.e. a deletion/insertion (indel) (see Deletion-Insertion and Description - Note). When phase information is not available, the variant should be described as NG_012232.1:g.12G>T(;)13C>G (see Alleles).

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
13
Q

The BRCA1 coding DNA reference sequence NM_007294.3 from position c.2074 to c.2080 is ..CATGACA.. A variant frequently found in the population is ..CATAACA.. (NM_007294.3:c.2077G>A). In a patient I found the sequence ..CATATAACA.. Can I describe this variant as NM_007294.3:c.[2077G>A;2077_2078insTA]?

A

The correct description of this variant is NM_007294.3:c.2077delinsATA.
NOTE: the answer was modified, i.e. the addition “However, since the variant is likely a combination of two other variants it is acceptable to describe it as NM_007294.3:c.[2077G>A;2077_2078insTA]” was removed.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
14
Q

a deletion of the T at position g.19 in the sequence AGAATCACA to AGAA_CACA
NOTE: the recommendation is not to describe the variant as NG_012232.1:g.19delT, i.e. describe the deleted nucleotide sequence. This description is longer, it contains redundant information and chances to make an error increases (e.g. NG_012232.1:g.19delG).

A

one nucleotide - NG_012232.1:g.19del

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
15
Q

a deletion of nucleotides g.19 to g.21 in the sequence AGAATCACA to AGAA___CA

A

NG_012232.1:g.19_21del

NOTE: the recommendation is not to describe the variant as NG_012232.1:g.19_21delTCA, i.e. describe the deleted nucleotide sequence. This description is longer, it contains redundant information and chances to make an error increases (e.g. NG_012232.1:g.19_21delTTA).

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
16
Q

a deletion of nucleotides c.183 to c.186+48 (coding DNA reference sequence), crossing an exon/intron border

A

NG_012232.1(NM_004006.1):c.183_186+48del

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
17
Q

the deletion of the T nucleotide at the exon/exon border in the sequence ..GAT gta..//..cag TCA.. changing to ..GA_ gta..//..cag TCA..

A

LRG_199t1:c.3921del

NOTE : according to an exception of the 3’rule the variant (NC_000023.10:g.32459297del) is not described as c.3922del since this would shift the position of the variant to the next exon (c. 3922 linking to g.32456507) (see exception in Numbering and see Q&A)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
18
Q

the deletion of the G nucleotide at the exon/intron border in the sequence GAACAGgt…/..agTGCCTT changing to GAACAG_t…/..agTGCCTT (not c.1704del)

A

LRG_199t1:c.1704+1del

NOTE: this description does not depend on the effect observed on RNA level, giving either altered splicing or r.1704del

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
19
Q

the deletion of the G nucleotide at the intron/exon border in the sequence CTGGCCgt…/..agGTTTTA changing to CTGGCCgt…/..ag_TTTTA (not c.1813-1del)

A

LRG_199t1:c.1813del

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
20
Q

a deletion of nucleotides c.4072-1234 to c.5155-246 removing exon 30 (starting at position c.4072) to exon 36 (ending at position c.5154) of the DMD-gene.

A

NG_012232.1(NM_004006.1):c.4072-1234_5155-246del

NOTE : c.4072-1234_5155-246delXXXXX, the size of the deletion (XXXXX) should not be described

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
21
Q

a deletion of exon 30 (starting at position c.4072) to exon 36 (ending at position c.5154) of the DMD-gene. The deletion break point has not been sequenced. Exons 29 (ending at c.4071) and 37 (starting at nucleotide c.5155) have been tested an shown to be not deleted. The deletion therefore starts in intron 29 (position c.4071+1 to c.4072-1) and ends in intron 36 (position c.5154+1 to c.5155-1).

A

NG_012232.1(NM_004006.1):c.(4071+14072-1)(5154+1_5155-1)del

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
22
Q

probe-based description of a deletion, identified by MLPA, of exon 30 (deleted position tested c.4196) to exon 36 (deleted position tested c.5090) of the DMD-gene. The deletion break point has not been sequenced. Exons 29 (position tested c.3996) and 37 (position tested c.5284) are not deleted.

A

NG_012232.1(NM_004006.1):c.(39964196)(5090_5284)del

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
23
Q

a deletion of nucleotides c.720 to c.991 starting in exon 8 (position c.720) and ending in exon 10 (position c.991) of the DMD-gene.

A

LRG_199t1:c.720_991del

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
24
Q

a deletion of the entire DMD gene based on a SNP-array analysis where the maximum size of the deletion lies between SNPs rs396303 and rs7887548 (nucleotides 31060227 and 33417151) and the minimum size between SNPs rs808178 and rs7887103 (nucleotides 31100351 and 33274278).

A

NC_000023.11:g.(3106022731100351)(33274278_33417151)del

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
25
Q

a deletion of the entire DMD gene based on a MLPA assay where the nucleotide positions g.31120496 and g.33339477 are defined by the 3’ nucleotide of the genomically most 5’ located probes (usually the ligation site) for the resp. last and first (brain promoter) exons.

A

NC_000023.11:g.(?31120496)(33339477_?)del

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
26
Q

a mosaic case where from position g.19 to g.21 besides the normal sequence also chromosomes are found containing a deletion of this sequence

A

NG_012232.1:g.19_21=/del

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
27
Q

a chimeric case, i.e. the sample is a mix of cells containing g.19_21= and g.19_21del

A

NG_012232.1:g.19_21=//del

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
28
Q

What is duplication in nucleotide?

A

a sequence change where, compared to a reference sequence, a copy of one or more nucleotides are inserted **directly 3’ **of the original copy of that sequence.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
29
Q

the duplication of a T at position c.20 in the sequence AGAAGTAGAGG to AGAAGTTAGAGG

A

NM_004006.2:c.20dup (NC_000023.10:g.33229410dup)

NOTE: it is not allowed to describe the variant as c.19_20insT (see prioritisation)
NOTE: the recommendation is not to describe the variant as NM_004006.2:c.20dupT, i.e. describe the duplicated nucleotide sequence. This description is longer, it contains redundant information and chances to make an error increases (e.g. NM_004006.2:c.20dupG).

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
30
Q

a duplication from position c.20 to c.23 in the sequence AGAAGTAGAGG to AGAAGTAGATAGAGG

A

NM_004006.2:c.20_23dup (NC_000023.10:g.33229407_33229410dup)

NOTE: the recommendation is not to describe the variant as c.20_23dupTAGA, i.e. describe the duplicated nucleotide sequence. This description is longer, it contains redundant information and chances to make an error increases (e.g. c.20_23dupTGGA).

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
31
Q

a duplication of nucleotides c.160 to c.264+48 (coding DNA reference sequence), crossing an exon/intron border

A

LRG_199t1:c.260_264+48dup (NC_000023.10:g.32862852_32862904dup)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
32
Q

the duplication of the T nucleotide at the exon/exon border in the sequence ..GAT gta..//..cag TCA.. changing to ..GATT gta..//..cag TCA..
NOTE : according to an exception of the 3’rule the variant (NC_000023.10:g.32459297dup) is not described as c.3922dup since this would shift the position of the variant to the next exon (c. 3922 linking to g.32456507)

A

LRG_199t1:c.3921dup

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
33
Q

the duplication of the G nucleotide at the exon/intron border in the sequence GAACAGgt…/..agTGCCTT changing to GAACAGggt…/..agTGCCTT (not c.1704dup)
NOTE: this description does not depend on the effect observed on RNA level, giving either altered splicing or r.1704dup

A

LRG_199t1:c.1704+1dup

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
34
Q

the duplication of the G nucleotide at the intron/exon border in the sequence CTGGCCgt…/..agGTTTTA changing to CTGGCCgt…/..agGGTTTTA (not c.1813-1dup)
NOTE: this description does not depend on the effect observed on RNA level, giving either altered splicing or r.1813dup

A

LRG_199t1:c.1813dup

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
35
Q

a duplication of nucleotides c.4072-1234 to c.5155-246 duplicating exon 30 (starting at position c.4072) to exon 36 (ending at position c.5154) of the DMD-gene.
NOTE : the format c.4072-1234_5155-246dupXXXXX, with XXXXX indicating the size of the duplication, should not be used
NOTE : the description NM_004006.2:c.4072-1234_5155-246dup is not correct, the reference sequence NM_004006.2 is a coding DNA reference sequence which does not include the intron sequences involved

A

LRG_199t1:c.4072-1234_5155-246dup

36
Q

a duplication of nucleotides c.720 to c.991 starting in exon 8 (position c.720) and ending in exon 10 (position c.991) of the DMD-gene.

A

LRG_199t1:c.720_991dup

37
Q

a duplication of exon 30 (starting at position c.4072) to exon 36 (ending at position c.5145) of the human DMD-gene. The duplication break point has not been sequenced. Exons 29 (ending at c.4071) and 37 (starting at nucleotide c.5146) have been tested an shown to be not duplicated. The duplication therefore starts in intron 29 (position c.4071+1 to c.4072-1) and ends in intron 36 (position c.5145+1 to c.5156-1).
NOTE : this description is part of proposal SVD-WG003 (undecided).
NOTE : previously, the suggestion was made to describe such duplications using the format c.4072-?_5154+?dup. However, since c.4072-? indicates “to an unknown postion 5’ of c.4072” and c.5154+? “to an unknown postion 3’ of c.5154” this description is not correct when it is known that exons 29 and 37 are involved.

A

NG_012232.1(NM_004006.2):c.(4071+14072-1)(5154+1_5155-1)dup

38
Q

a triplication of the sequence from exon 30 (starting at position c.4072) to exon 36 (ending at position c.5154) of the DMD-gene (break points not sequenced).
NOTE : this description should only be used when the two additional copies are in tandem with the original copy. There is no specific recommendation yet how to describe such a change but following current recommendations the format would be something like g.?_?ins(3238107632382698)(32430031_32456357)[2] ([2] since 2 additional copies have been inserted somewhere in the genome).

A

NC_000023.10:g.(3238107632382698)(32430031_32456357)[3] (LRG_199t1:c.(4071+14072-1)(5154+1_5155-1)[3])

39
Q

a duplication of the entire DMD gene based on a SNP-array analysis where the maximum size of the duplication lies between SNPs rs396303 and rs7887548 (nucleotides 31060227 and 33417151) and the minimum size between SNPs rs808178 and rs7887103 (nucleotides 31100351 and 33274278). Describing the duplication based on a coding DNA reference sequence using NC_000023.11(NM_004006.2):c.(-205839-62966)(*21568*61692)dup makes no sense.
NOTE: the array analysis detects an extra copy of the sequences and it has to be determined whether it is a duplication. When it is not sure the variant is a duplication the variant should be described as an insertion, g.??insNC_000023.11:(3106022731100351)(33274278_33417151)

A

NC_000023.11:g.(3106022731100351)(33274278_33417151)dup

40
Q

a duplication of the entire DMD gene based on a MLPA assay where nucleotides g.31120496 and g.33339477 are the center of the probes for the resp. last and first (brain promoter) exons.
NOTE: the MLPA analysis detects an extra copy of the sequences and it has to be determined whether it is a duplication. When it is not sure the variant is a duplication the variant should be described as an insertion, g.??insNC_000023.11:(?31120496)(33339477?)

A

NC_000023.11:g.(?31120496)(33339477_?)dup

41
Q

a mosaic case where from position g.19 to g.21 besides the normal sequence also chromosomes are found containing a duplication of this sequence

A

NG_012232.1:g.19_21=/dup

42
Q

a chimeric case, i.e. the sample is a mix of cells containing g.19_21= and g.19_21dup

A

NG_012232.1:g.19_21=//dup

43
Q

the insertion of nucleotides CCT between nucleotides g.32862923 and g.32862924

A

NC_000023.10:g.32862923_32862924insCCT (LRG_199t1:c.240_241insAGG)

44
Q

the insertion of an T nucleotide between nucleotides g.32867861 and g.32867862

A

NC_000023.10:g.32867861_32867862insT (NM_004006.2:c.169_170insA)

45
Q

the insertion of a copy of nucleotids c.858 to c.895 between nuclotides c.849 and c.850

A

NM_004006.2:c.849_850ins858_895

46
Q

the insertion of nucleotides g.35788169 and g.35788352 as found in NC_000022.10 between nucloetides g.47643464 and g.47643465

A

NC_000002.11:g.47643464_47643465ins[NC_000022.10:35788169_35788352]

47
Q

the insertion of T followed by a copy of the sequence from c.401 to c.419 (a duplication not directly flanking the original sequence)

A

NM_004006.2:c.419_420ins[T;401_419]

48
Q

the insertion of T followed by a copy of the sequence from c.450 to c.470, followed by AGGG

A

LRG_199t1:c.419_420ins[T;450_470;AGGG]

49
Q

a copy of nucleotides c.850 to c.900 is inserted, in inverted orientation, 5’ of the original sequence, between nucleotide c.849 and c.850

A

NM_004006.2:c.849_850ins850_900inv

50
Q

a copy of nucleotides c.850 to c.900 is inserted, in inverted orientation, 3’ of the original sequence, between nucleotide c.900 and c.901

A

NM_004006.2:c.900_901ins850_900inv

51
Q

an inverted copy of nucleotides c.851 to c.940, with a G>A substitution of nucleotide c.884, is inserted directly 3’ of the original sequence

A

LRG_199t1:c.940_941ins[885_940inv;A;851_883inv]

52
Q

an inverted copy of nucleotides c.851 to c.940, with a deletion from nucleotides c.886 to c.902, is inserted directly 3’ of the original sequence

A

NM_004006.2:c.940_941ins[903_940inv;851_885inv]

53
Q

the insertion of a G at an unknown position in the sequence encoding amino acid 75

A

NM_004006.2:c.(222_226)insG (p.Asn75fs)

54
Q

the insertion of 12 nucleotides (not specified) at an unknown position between nucleotides g.3076562 and g.3076732 (exon 1 of the HTT gene containing the Gln/Pro repeat region)

A

NC_000004.11:g.(3076562_3076732)ins(12)

55
Q

the insertion of one not specified nucleotide (N) between position g.32717298 and g.32717299

A

NC_000023.10:g.32717298_32717299insN (NM_004006.2:c.761_762insN)

56
Q

the insertion of 5 not specified nucleotides (NNNNN) between position c.761 and c.762

A

NM_004006.2:c.761_762insNNNNN (alternatively NM_004006.1:c.761_762ins(5))

57
Q

the insertion of 100 nucleotides (not specified) between position g.32717298 and g.32717299

A

NC_000023.10:g.32717298_32717299ins(100)

58
Q

the insertion of 80 to 120 nucleotides between position g.32717298 and g.32717299

A

NC_000023.10:g.32717298_32717299ins(80_120)

59
Q

the insertion of an unknown number of nucleotides between position g.32717298 and g.32717299

A

NC_000023.10:g.32717298_32717299ins(?)

60
Q

the insertion of a sequence from the X-chromosome (NC_000023.10), maximally involving nucleotides 12345_45678 but certainly nucleotides 2345634567, at an unknown position (g.??) in the genome

A

g.?_?insNC_000023.10:(1234523456)(34567_45678)

61
Q

What is a delins?

A

A sequence change where, compared to a reference sequence, one or more nucleotides are replaced by one or more other nucleotides and which is not a substitution, inversion or conversion.

62
Q

The delins rule: two variants separated by one or more nucleotides should be described individually and not as a “delins”
Exception: two variants separated by one nucleotide, together affecting one amino acid, should be described as a “delins”
give an example

A

affecting same amino acid:
c.225_227delinsTAT (p.Lys79Tyr)

affecting different amino acids:
c.[225A>T;227G>T] (p.[Lys79*;Lys79Asn])

63
Q

a deletion of nucleotide g.32386323 (a T, not described), replaced by nucleotides GA
coding seq is c.4661 also write the c. nomenclature

A

NC_000023.11:g.32386323delinsGA

c.4661delinsTC

64
Q

a deletion of nucleotides c.6775 to c.6777 (GAG, not described), replaced by a C nucleotide

A

NM_004006.2:c.6775_6777delinsC

NOTE: the recommendation is not to describe the variant as NM_004006.2:c.6775_6777delGAGinsC, i.e. describe the deleted nucleotide sequence. This description is longer, it contains redundant information and chances to make an error increase (e.g. NM_004006.2:c.6775_6777delGTGinsC ).

65
Q

a deletion replacing nucleotides c.145 to c.147 (CGC, not described) with TGG, protein change from Arg to Trp at position 49

A

LRG_199t1:c.145_147delinsTGG (p.Arg49Trp)

66
Q

a deletion of nucleotides c.9002 to c.9009, replaced by nucleotides TTT

A

LRG_199t1:c.9002_9009delinsTTT

NOTE: two variants separated by one nucleotide, together affecting one amino acid, should be described as a “delins”, so the description c.[145C>T;147C>G] is not correct

67
Q

nucleotides g.pter to g.8247756 of chromosome 2 are deleted and replaced by nucleotides g.pter to g.1582566 of chromosome 11: the derivative chromosome 2 from an unbalanced translocation between the short arms of chromosomes 2 and 11 (ISCN der(2)t(2;11)(p25.1;p15.2)).

A

NC_000002.12:g.pter_8247756delins[NC_000011.10:g.pter_15825266]

NOTE: balanced translocations are described as two complementary “delins” variants.

68
Q

Q: The BRCA1 coding DNA reference sequence from position c.2074 to c.2080 is ..CATGACA.. A variant frequently found in the population is ..CATAACA.. (c.2077G>A). In a patient I found the sequence ..CATA TAACA.. how do we describe this?

A

NM_007294.3:c.2077delinsATA

69
Q

What is HGVS is allele?

A

a series of variants on one chromosome.

70
Q

what is the general equition to write for one allele?

A

Format (one allele): “prefix”[“change1”;”change2”],

g.[123G>A;345del]

71
Q

what is the general rule to write for two alleles?

A

“prefix”[“change”];[“change”],

g.[123G>A];[345del]

72
Q

What is the rule when it is not known whether these are on one chromosome (in cis) or on different chromosomes (in trans)?

A

“variant1(;)variant2”, i.e. without using “[ ]”

73
Q

one allele (chromosome) of a gene contains two different changes, c.2376G>C and c.3103del. The variants are found in cis.

A

LRG_199t1:c.[2376G>C;3103del]

74
Q

one allele (X-chromosome) contains two different variants in two different genes, g.30683643A>G in the GK gene and g.33038273T>G in the DMD gene.

A

NC_000023.10:g.[30683643A>G;33038273T>G]

75
Q

one allele (chromosome 3) contains a repeated AGC tri-nucleotide sequence, starting at position g.6391268, containing 50 to 60 AGC copies

A

NC_000003.12:g.63912687AGC[(50_60)]

76
Q

one allele (chromosome 3) contains a repeated AGC tri-nucleotide sequence, starting at position g.6391268, containing 60 or more AGC copies

A

NC_000003.12:g.63912687AGC[(60_?)]

77
Q

the two alleles (chromosomes) of a gene each contain a different change, c.2376G>C and c.3103del. The variants are found in trans. A heterozygous case (compound heterozygote, e.g. in a recessive disease).

A

LRG_199t1:c.[2376G>C];[3103del]

78
Q

both alleles (chromosomes) of a gene contain the same variant, c.2376G>C. A homozygous case (e.g. in a recessive disease).

A

LRG_199t1:c.[2376G>C];[2376G>C]

79
Q

a sample contains variants c.296T>G and c.1083A>C on both alleles (chromosomes) and variant c.476C>T on only one allele.

A

LRG_199t1:c.[296T>G;476T>C;1083A>C];[296T>G;1083A>C]

80
Q

one allele (chromosome) of a gene contains a variant, c.2376G>C, the other allele (chromosome) contains the reference sequence, c.2376= (is wild-type).

A

LRG_199t1:c.[2376G>C];[2376=]

81
Q

one allele (chromosomes) of a gene contains a variant, c.2376G>C, while a variant for the other allele is expected but not yet identified (c.?) (e.g. in individuals affected by a recessive disease).

A

LRG_199t1:c.[2376G>C];[?]

82
Q

two variants in a gene, c.2376G>C and c.3103del, but it is not known whether they are on the same or on different alleles (chromosomes).

A

LRG_199t1:c.2376G>C(;)3103del

83
Q

a sample contains a homozygous variant (c.476T>C) and two heterozygous variants (c.296T>G and c.1083G>C) for which it is not known on which allele (chromosome) they are (although at least one, in the example c.296T>G, is on the same allele as c.476T>C).

A

NM_004006.2:c.[296T>G;476T>C];[476T>C] (;)1083A>C

84
Q

a sample contains heterozygous variants on different alleles (c.296T>G and c.476T>C) and two additional heterozygous variants (c.1083G>C and c.1406del) for which it is not known on which allele (chromosome) they are.

A

LRG_199t1:c.[296T>G];[476T>C]
(;)1083G>C(;)1406del

85
Q
A

HGVS (2 decks)

Brainscape helps you reach your goals faster, through stronger study habits.
© 2024 Bold Learning Solutions. Terms and Conditions