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LYFE SCIENCES
Project: HERA
NM_000179.3:c.866G>A
p.Gly289Asp  ·  MSH6
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Classification rationale
1

The MSH6 c.866G>A (p.Gly289Asp; p.G289D) variant has not been observed in COSMIC and has been reported in ClinVar with conflicting germline classifications, including uncertain significance, likely benign, and benign submissions.

clinvar ↗
2

This variant is present in gnomAD v4.1 at an allele frequency of 0.000216846 (350/1614052 alleles) with grpmax filtering allele frequency 0.00024593, which exceeds the MSH6 BS1 threshold of 0.00022 but remains below the BA1 threshold of 0.0022.

gnomad_v4 ↗ cspec ↗
3

Computational data support a benign interpretation: the MSH6 HCI prior probability is 0.0021, below the BP4 threshold of 0.11, SpliceAI predicts no significant splice impact with a max delta score of 0.01, and additional predictors are not strongly damaging (REVEL 0.272; BayesDel -0.256015).

spliceai ↗ cspec ↗
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
  • —
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= 9.20165e-05; MAF= 0.00920%, 26/282558 alleles, homozygotes = 0) and has highest observed frequency in the European (non-Finnish) population (AF= 0.000193865; MAF= 0.01939%, 25/128956 alleles, homozygotes = 0); grpmax FAF= 0.00012357.
gnomAD v4.1This variant is present in gnomAD v4.1 (AF= 0.000216846; MAF= 0.02168%, 350/1614052 alleles, homozygotes = 0) and has highest observed frequency in the Remaining individuals population (AF= 0.00040009; MAF= 0.04001%, 25/62486 alleles, homozygotes = 0); grpmax FAF= 0.00024593.
gnomAD v2 ↗ gnomAD v4 ↗
ClinVar evidence
02
ClinVar
This variant has been reported in ClinVar as Uncertain significance (3 clinical laboratories) and as Benign (1 clinical laboratory) and as Likely benign (1 clinical laboratory). (ClinVarID = 627661)
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. MSH6, a DNA mismatch repair protein, is frequently mutated in colorectal, small bowel, and endometrial cancers.
OncoKB ↗
In silico evidence
04
In silico
SpliceAI predicts no significant splice impact for this variant (max delta score = 0.01). REVEL score = 0.272. BayesDel score = -0.256015. HCI prior probability for pathogenicity = 0.0021. MAPP score = 3.78. Custom PP2 score = 0.001.
SpliceAI ↗
COSMIC evidence
05
COSMIC
This variant does not lie in a statistically significant hotspot. This variant has not previously been reported in somatic cancers (COSMIC).
COSMIC ↗
Cancer hotspots evidence
06
Cancer hotspots Not found
This variant does not lie in a statistically significant hotspot.
ResidueG289
Hotspots ↗