Duncan - variant nomenclature and analysis Flashcards

Question

what are the five classifications that a variant can fall into?

Answer 1

class 1 - benign class 2 - likely benign class 3 - VUS class 4 - likely pathogenic class 5 - pathogenic

Answer 2

Class 1 - benign Seen in high frequencies in the population (normally) Some experimental evidence showing the variant does not have an ‘adverse’ effect on the protein. Not linked to patient phenotype Class 2 - likely benign This means they are benign, but the evidence is less strong than for class one variants. So seen in normal population, but not as frequently as a class one variant, often not located in a functional domain of the protein 1 and 2 not reported to patient - not related to disease

Answer 3

Class 3 - unknown significance Evidence for P or B is inconclusive - variants of unknown significance Awkward to report to patients - doesn't give diagnosis or confirm that they don't have a pathogenic mutation Often further work needed, such as testing more genes, or checking whether affected and unaffected family members also have the variant Those closer to class 4 are reported, those closer to class 2 are not. I.e. you report these when you think further evidence will confirm the variants are pathogenic. If not you're just causing anxiety for the patient

Answer 4

you cannot exclude genetic disorders. Just because you haven't yet found a pathogenic variant. You can only confirm genetic disorders

Answer 5

Class 4 - likely pathogenic No/low population frequency Previous pathogenic variants in the region may have been identified before Class 5 - pathogenic Segregates with the disease in family (seen in a family only in members with the disease) Functional study/experiments show the protein isn't working properly/confirms adverse effects All evidence in agreement Truncating change - is often class 5, due to nonsense variants or frameshift-causing ones, you lose a chunk of the protein and its likely to cause a problem… 4 and 5 reported to patient and clinicians as confirms a genetic diagnosis of disease and may help with treatment/allow for family testing/inform on risks to offspring

Answer 6

frequency/how common the variant is in normal population How the protein structure/function is affected Does it result in LOF/altered properties, or alter splicing? Has it been identified in other patients with the same disease Has it been inherited, or newly arisen (de novo), and if inherited, do other family members with the variant also have the disease? Does it make sense - i.e., is the function of the gene/protein in question linked to the patient’s clinical symptoms? Is the variant in a mutational hotspot/vital functional protein domain (regions where any changes often result in disease because the correct sequence is so important)?

Answer 7

The type of variant can be a major clue - Nonsense / frameshift-causing variants = often pathogenic as result in a truncated protein that is severely affected Synonymous/silent - almost always benign obviously Missense - depends on how drastic the amino acid change is. Was it a swap to another amino acid with similar properties? Or is it different in size/charge/hydrophobic and likely to affect DNA binding/protein folding + shape etc...

Answer 8

You look in databases like Gnomad, with loads of variants collected from loads of whole genome sequencing projects that only involved people free of severe disease (as far as could be told), and see how common your variant in question is in the healthy population If the variant is found in healthy population - you CANNOT apply ‘PM2’, and it’s unlikely/less likely to be pathogenic If the variant is not found in healthy population - you CAN apply ‘PM2’ BA1 = when the variant is in >5% of general population (highly unlikely to cause disease you don't see more than 5% of people with a certain rare genetic disorder) therefore is benign, typically filtered out in the first place when sequencing results) stand alone, if BA1 is applicable its enough to classify a variant as benign Caveat - can see high frequencies of disease causing variants in recessive genes in heterozygotes, e.g. CFTR pathogenic variants seen in 1 in 25 BS1 - similar, but less ‘strong’. Applied to variants when the allele frequency is greater than expected for that of the disorder Can only be used when you’ve got knowledge of the disease occurrence /frequency (on top of frequency of the variant in normal population). Yoy can apply BS1 if the frequency of the variant is higher than the frequency of the disease

Answer 9

Can be applied to recessive genes if - there are no homozygotes of the variant in Gnomad/the normal control populations and frequency of the variant is less than that of the disease incidence

Answer 10

an algorithm uses information to determine whether the amino acid change/s seen in a variant will affect the gene product/protein 1. Look at if there are changes to evolutionarily conserved sites - as in if the amino acid that's been altered is one that's the same across a load of species, it's probably very important for structure/function that it stays as that amino acid. It's not as much of a concern if its at a site that's more flexible where species have some different amino acids there 2. Also takes into account what the amino acid changed to and from - were they of similar size/charge/hydrophobicity etc… because the more they differ in properties, the more likely that variant is to alter protein shape/structure/function gives you a revel score: 0 to 0.39 = Benign 0.4 to 0.69 = uncertain 0.7 to 1 = pathogenic

Answer 11

0 to 0.39 = Benign 0.4 to 0.69 = uncertain 0.7 to 1 = pathogenic PP3 may only be applied with a pathogenic score BP4 maybe be applied with a Benign score

Answer 12

truncated proteins, so nonsense variants or variants resulting in a frameshift. apply PVS (pathogenic very strong) NMD Some variants are likely to escape the process and survive if: DNA variant is present in last exon DNA variant in located in last 50 nucleotides of the penultimate exon If it escapes the truncated version might function enough to not cause disease or a milder disease at least if don't escape = massively reduced CN = disease causing

Answer 13

if donor or acceptor sites are altered, this is computational evidence supportying a deleterious effect of a gene (PP3) AND - especially in donor site, inclusion of intron etc... - can get frameshift, early stop codon, truncated protein, NMD so apply PVS benign counterparts - BP4 (computational evidence suggests no impact on gene/ gene product And/or BP7 yadyadyada

Answer 14

If you test mum and dad and it looks like they don't have it (so it is de novo) but you haven't confirmed they are indeed the mum and dad (well really that dad is dad) you apply PM6 If testing mum and dad tells you it’s de novo, plus no family history of the disease, and you have confirmed paternity (and maternity) by e.g. QF-PCR, you apply PS2

Answer 15

Litch so simple, you test the family for the variant and ask the question “is the disease always and only seen in members with the variant?” if yes, its very likely it causes the disease, that to have the disease one must inherit the variant You can apply PP1 if it is the case, and BS4 if its not (cus if family members without the disease do have the variant its a pretty strong indicator that the variant does not cause the disease)

Answer 16

Does the patient’s symptoms align with the affected gene and associated disease? E.g. A patient referred with learning disability but the gene we found a variant in is only associated with short limbs Does not support pathogenicity E.g. A patient referred with learning disability and the gene with the variant is commonly reported in patients with learning disability Supports pathogenicity, apply PP4

Answer 17

Basically is there reason to believe a mutation in that specific location is likely to cause disease - e.g. a region that is so vital to function, variants there are often pathogenic Can use disease databases to find where pathogenic variants are in a disease and identify hotspots - often super important domains of a protein, e.g. DNA binding sites Apply PM1