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LYFE SCIENCES
Project: HERA
NM_001127500.3:c.110T>C
p.Val37Ala  ·  MET
ACMG/AMP
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Classification rationale
1

The MET c.110T>C (p.Val37Ala) variant has been reported in ClinVar with likely benign and benign submissions.

clinvar ↗
2

This variant is present in population databases at a frequency above the BS1 threshold, with the highest observed frequency of 0.70588% in South Asian individuals in gnomAD v2.1 and 0.68732% in South Asian individuals in gnomAD v4.1, arguing against a rare pathogenic germline variant.

gnomad_v2 ↗ gnomad_v4 ↗
3

No well-established variant-specific functional study was identified to support either a damaging or a normal effect.

oncokb ↗
4

Computational evidence supports a benign interpretation, with SpliceAI predicting no significant splice impact (maximum delta score 0.00), REVEL of 0.142, and BayesDel of -0.247812.

spliceai ↗
Applied criteria
Met
Not met
Not assessed
N/A
Very strong
Strong
Moderate
Supporting
Pathogenic evidence
PVS
PVS1
PS
PS1
PS2
PS3
PS4
PM
PM1
PM2
PM3
PM4
PM5
PM6
PP
PP1
PP2
PP3
PP4
PP5
Benign evidence
BA
BA1
BS
BS1
BS2
BS3
BS4
BP
BP1
BP2
BP3
BP4
BP5
BP6
BP7
PVS1
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Rationale
Select a criterion to inspect its explanation.
Evidence used
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Gaps remaining
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Rule
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Publications
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Research and evidence
gnomAD v2.1 evidence
v2.1
gnomAD v4.1 evidence
v4.1
01
Population
gnomAD v2.1This variant is present in gnomAD v2.1 (AF= 0.000908223; MAF= 0.09082%, 255/280768 alleles, homozygotes = 1) and has highest observed frequency in the South Asian population (AF= 0.00705882; MAF= 0.70588%, 216/30600 alleles, homozygotes = 1); grpmax FAF= 0.0062877.
gnomAD v4.1This variant is present in gnomAD v4.1 (AF= 0.000544625; MAF= 0.05446%, 879/1613956 alleles, homozygotes = 10) and has highest observed frequency in the South Asian population (AF= 0.00687323; MAF= 0.68732%, 626/91078 alleles, homozygotes = 10); grpmax FAF= 0.00642681.
gnomAD v2 ↗ gnomAD v4 ↗
ClinVar evidence
02
ClinVar
This variant has been reported in ClinVar as Likely benign (6 clinical laboratories) and as Benign (3 clinical laboratories). (ClinVarID = 41610)
ClinVar ↗
Functional evidence
03
Functional
OncoKB: Unknown Oncogenic Effect
OncoKB did not identify variant-specific reviewed functional evidence for this variant; gene-level curated context is available for reviewer follow-up. MET, a receptor tyrosine kinase, is recurrently altered by mutation or amplification in various cancer types.
OncoKB ↗
In silico evidence
04
In silico
SpliceAI predicts no significant splice impact for this variant (max delta score = 0.00). REVEL score = 0.142. BayesDel score = -0.247812.
SpliceAI ↗
COSMIC evidence
05
COSMIC
This variant does not lie in a statistically significant hotspot. This variant has previously been reported in somatic cancers (COSMIC; COSV104627100, n = 1 times).
COSMIC ↗
Cancer hotspots evidence
06
Cancer hotspots Not found
This variant does not lie in a statistically significant hotspot.
ResidueV37
Hotspots ↗