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MSH6
Final classification
VUS
MSH6 c.1822A>G · p.Ile608Val
MSH6

NM_000179.3:c.1822A>G (p.Ile608Val) is a missense variant in exon 4 of MSH6. Only one criterion is met: BP4_supporting based on an HCI prior probability of 0.0038 (<0.11), with concordant in silico predictions (REVEL 0.185, BayesDel -0.360, SpliceAI Δ=0.01). All other applicable criteria are not met, and no pathogenic criteria are met.

Gene
MSH6
Transcript
NM_000179.3
HGVS · transcript:coding
NM_000179.3:c.1822A>G
Consequence
N/A
GRCh38
chr2:47799805 A>G
GRCh37
chr2:48026944 A>G
Basis ClinGen InSiGHT Hereditary Colorectal Cancer/Polyposis Expert Panel Specifications to the ACMG/AMP Variant Interpretation Guidelines for MSH6 Version 2.0 v2.0 criteria-combination framework was evaluated deterministically with applied criteria: BP4 supporting; no rule matched the adjudicated criteria.
ClinGen InSiGHT Hereditary Colorectal Cancer/Polyposis Expert Panel Specifications to the ACMG/AMP Variant Interpretation Guidelines for MSH6 Version 2.0 v2.0 criteria-combination framework was evaluated deterministically with applied criteria: BP4 supporting; no rule matched the adjudicated criteria.
Classification rationale
BP4 VUS
MSH6 c.1822A>G

NM_000179.3:c.1822A>G (p.Ile608Val) is a missense variant in exon 4 of MSH6. Only one criterion is met: BP4_supporting based on an HCI prior probability of 0.0038 (<0.11), with concordant in silico predictions (REVEL 0.185, BayesDel -0.360, SpliceAI Δ=0.01). All other applicable criteria are not met, and no pathogenic criteria are met.1 This variant has been observed in gnomAD v4.1 at a grpmax FAF of 6.393e-05 (100/1,614,126 alleles, 0 homozygotes), which is above the VCEP PM2_supporting threshold of 0.00002 but below the benign BA1 (0.0022) and BS1 (0.00022) thresholds. The variant is present at low frequency in population databases, consistent with a rare variant of uncertain significance.2 This variant has been reported in ClinVar as Uncertain significance by 10 of 11 clinical submitters and as Likely benign by 1 submitter (ClinVar Variation ID: 182626). No expert panel classification exists, and the review status is 'criteria provided, single submitter.' The variant has not been reported in COSMIC.3 No functional assay data are available for this variant in the InSiGHT MMR calibrated functional assay documentation. The variant was predicted to have 'no impact on MSH6' by the CoDP in silico tool (score 0.033; PMID:23621914), but this is computational prediction, not experimental functional evidence.4 Overall, NM_000179.3:c.1822A>G (p.Ile608Val) is classified as a Variant of Uncertain Significance (VUS) under the InSiGHT MSH6 VCEP v2.0 framework. Only BP4_supporting is met; all other applicable criteria are not met. No pathogenic criteria are met, and no benign criteria beyond BP4_supporting apply.5

BP4 VUS
1 hci_priorrevelbayesdelspliceai ↗cspec ↗
4 vcep_functional_assay_svi_documentation_mmrPMID:23621914 ↗
Gene diagram · NM_000179.3 · variants mapped to exon structure
MSH6 NM_000179.3
Fetching transcript structure from UCSC…
Applied criteria · 1 applied · 15 assessed
Applied · 1
Strength Supporting Moderate Strong Very strong
BP4 supporting Benign
BP4_supporting is met under the InSiGHT MSH6 VCEP v2.0: the HCI prior probability for pathogenicity is 0.0038, which is below the <0.11 threshold. Multiple independent in silico predictors support a benign interpretation: REVEL score 0.185 (low pathogenicity), BayesDel score -0.360 (benign), and SpliceAI max delta 0.01 (no predicted splicing impact).
HCI prior probability = 0.0038 (<0.11 threshold for BP4_supporting per VCEP)REVEL score = 0.185 (low)BayesDel score = -0.360
Assessed · not applied
Pathogenic
PS1 No different underlying nucleotide change encoding the same amino acid substitution (p.Ile608Val) has been classified as Pathogenic or Likely Pathogenic by the InSiGHT MSH6 VCEP.
PS2 No de novo observations were identified for NM_000179.3:c.1822A>G in the available evidence.
PS3 No calibrated functional assay data exist for NM_000179.3:c.1822A>G (p.Ile608Val).
PM2 PM2_supporting requires gnomAD v4 grpmax filtering allele frequency < 0.00002 (<1 in 50,000 alleles) per InSiGHT MSH6 VCEP.
PM5 PM5 requires a different missense change at the same amino acid residue (Ile608) classified as Pathogenic or Likely Pathogenic by the VCEP, AND PP3 must be supporting.
PP1 No co-segregation data are available for NM_000179.3:c.1822A>G.
PP3 PP3 requires HCI prior probability > 0.68 for supporting or > 0.81 for moderate per InSiGHT MSH6 VCEP.
PP4 No tumor data (MSI status or MMR IHC) are available for patients carrying NM_000179.3:c.1822A>G.
Benign
BA1 BA1 requires gnomAD v4 grpmax filtering allele frequency ≥ 0.0022 (0.22%) per InSiGHT MSH6 VCEP.
BS1 BS1 requires gnomAD v4 grpmax filtering allele frequency ≥ 0.00022 (0.022%) and < 0.0022 per InSiGHT MSH6 VCEP.
BS2 No evidence of co-occurrence in trans with a known pathogenic MSH6 variant in a patient with colorectal cancer after age 45 without CMMRD features.
BS3 No calibrated functional assay data demonstrate proficient MMR function (functional odds ≤ 0.05 for BS3_strong or ≤ 0.48 for BS3_supporting) for NM_000179.3:c.1822A>G.
BS4 No lack-of-segregation data are available.
BP5 No tumor data (MSS status or MMR IHC) are available for patients carrying NM_000179.3:c.1822A>G.
BP7 BP7 applies only to synonymous (silent) or intronic variants at or beyond -21/+7.
N/A · 12 PVS1 · PS4 · PM1 · PM3 · PM4 · PM6 · PP2 · PP5 · BP1 · BP2 · BP3 · BP6
Research & evidence
Population frequency
gnomAD v4.1 screenshot
gnomAD v4.1
gnomAD v2.1 screenshot
gnomAD v2.1
v4.1
This variant is present in gnomAD v4.1 (AF= 6.1953e-05; MAF= 0.00620%, 100/1614126 alleles, homozygotes = 0) and has highest observed frequency in the Remaining individuals population (AF= 0.000112018; MAF= 0.01120%, 7/62490 alleles, homozygotes = 0); grpmax FAF= 6.393e-05.
v2.1
This variant is present in gnomAD v2.1 (AF= 2.83724e-05; MAF= 0.00284%, 8/281964 alleles, homozygotes = 0) and has highest observed frequency in the European (non-Finnish) population (AF= 5.43225e-05; MAF= 0.00543%, 7/128860 alleles, homozygotes = 0); grpmax FAF= 2.298e-05.
🇨🇦 CA
Absent from gnomAD-Canada v1.0.
Allele frequency by ancestry
three datasets · side by side
gnomAD v4.1
0.0062% · 100 / 1,614,126
0 hom · FAF 0.0064%
Remaining individuals
7 / 62,490
0.011%
European (non-Finnish)
91 / 1,180,042
0.0077%
African/African American
2 / 74,952
0.0027%
+ 7 not observed (Admixed American, European (Finnish), Amish, East Asian, Middle Eastern, South Asian, Ashkenazi Jewish)
gnomAD v2.1
0.0028% · 8 / 281,964
0 hom · FAF 0.0023%
European (non-Finnish)
7 / 128,860
0.0054%
European (Finnish)
1 / 25,120
0.004%
+ 6 not observed (African/African American, Admixed American, Ashkenazi Jewish, East Asian, Remaining individuals, South Asian)
gnomAD Canada 🇨🇦
Absent · 0 / ?
0 hom
Not observed in any ancestry group.
ClinVar screenshot
ClinVar
This variant has been reported in ClinVar as Uncertain significance (9 clinical laboratories) and as Uncertain Significance (1 clinical laboratory) and as Likely benign (1 clinical laboratory). (ClinVarID = 182626)
SpliceAI screenshot
In silico
SpliceAI predicts no significant splice impact for this variant (max delta score = 0.01). REVEL score = 0.185. BayesDel score = -0.360174. HCI prior probability for pathogenicity = 0.0038. MAPP score = 4.95. Custom PP2 score = 0.003.
Functional / OncoKB screenshot
Functional 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 ↗
COSMIC screenshot
COSMIC
Cancer hotspots screenshot
Cancer hotspots
Somatic evidence Not in COSMIC / hotspots
COSMIC
This variant does not lie in a statistically significant hotspot. This variant has not previously been reported in somatic cancers (COSMIC).
Hotspots
This variant does not lie in a statistically significant hotspot.
Sources & reference links
9Sources
CSpec VCEP
ClinVar
gnomAD v2.1
gnomAD v4.1
gnomAD-Canada
SpliceAI
OncoKB
COSMIC
Cancer hotspots
Triaged references · 9 PMIDs not cited in assessment
22949379 ↗ A multifactorial likelihood model for MMR gene variant classification incorporating probabilities based on sequence bioinformatics and tumor characteristics: a report from the Colon Cancer Family Registry. CLINVAR
25741868 ↗ Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology. CLINVAR
26467025 ↗ A Standardized DNA Variant Scoring System for Pathogenicity Assessments in Mendelian Disorders. CLINVAR
30374176 ↗ Outcomes of 92 patient-driven family studies for reclassification of variants of uncertain significance. CLINVAR
11598466 ↗ Practice parameters for the identification and testing of patients at risk for dominantly inherited colorectal cancer--supporting documentation. CLINVAR
20301390 ↗ Lynch Syndrome. CLINVAR
23621914 ↗ CoDP: predicting the impact of unclassified genetic variants in MSH6 by the combination of different properties of the protein. CLINVAR
23788249 ↗ ACMG recommendations for reporting of incidental findings in clinical exome and genome sequencing. CLINVAR
28492532 ↗ Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria. CLINVAR