Variant classification summary

NM_000251.3:c.1316_1318del

MSH2 · NP_000242.1:p.(Pro439del) · NM_000251.3

GRCh37: chr2:47672722 ACTC>A · GRCh38: chr2:47445583 ACTC>A

Gene: MSH2 Transcript: NM_000251.3

Final call

VUS

PM2 supporting

Variant details

Gene

MSH2

Transcript

NM_000251.3

Protein

NP_000242.1:p.(Pro439del)

gnomAD AF

ClinVar

Uncertain significance

OncoKB

Unknown Oncogenic Effect

Classification rationale

Interpretation summary

Generated evidence synthesis

1

NM_000251.3:c.1316_1318del is an in-frame deletion of 3 nucleotides in exon 8 of MSH2, resulting in p.Pro439del. This variant is absent from all population databases including gnomAD v2.1, v4.1, and gnomAD-Canada, meeting the InSiGHT MSH2 VCEP v2.0.0 PM2_Supporting criterion.

2

The InSiGHT MSH2 VCEP v2.0.0 declares multiple criteria as not applicable for MMR gene classification: PM1 (no recognized mutational hotspots), PM4 (protein length change from in-frame variants not used), PS4 (IHC data preferred over proband counting), PP5, BP6, BP1, BP2, BP3, PM6, and PP2.

3

PVS1 is not applicable to this in-frame deletion under VCEP rules as it does not introduce a premature termination codon, does not involve canonical splice sites, and no patient mRNA assay data is available. PS1 and PM5 are not applicable as they are defined for missense substitutions only.

4

PP3 and BP4 are not applicable to this in-frame deletion under VCEP rules, which specify HCI prior thresholds for missense variants and SpliceAI thresholds for intronic/synonymous variants. SpliceAI predicts no splicing impact (max delta = 0.01), consistent with the variant's location within exon 8 and its in-frame nature.

5

No functional assay data (PS3/BS3), segregation data (PP1/BS4), tumor phenotype data (PP4/BP5), de novo reports (PS2), or trans co-occurrence data (BS2) are available for this variant. The ClinVar entry (Variation ID 90623) reports classifications of Uncertain significance by 4 clinical laboratories and Likely pathogenic by 2 laboratories, with review status 'criteria provided, single submitter' at the star-level aggregate.

6

Eight publications were reviewed for this variant, including full-text analysis where available. None of the reviewed publications mention NM_000251.3:c.1316_1318del specifically. The publications include methodological papers (SIFT Indel), ACMG/AMP guideline documents, Lynch syndrome management guidelines, and hereditary cancer syndrome reviews.

7

Based on the InSiGHT MSH2 VCEP v2.0.0 framework, the only applicable criterion met is PM2_Supporting (absent from gnomAD). With a single supporting pathogenic criterion and no benign criteria, the evidence is insufficient for classification beyond Variant of Uncertain Significance per the VCEP combination rules. Additional evidence from tumor studies, segregation analysis, or functional assays would be required to reach a more definitive classification.

Final determination: No criteria-combination rule matched the adjudicated criteria in the Richards et.al., 2015 - Combining rules v2.0.0 framework, so the variant remains a Variant of Uncertain Significance pending human review.

Criteria assessment

ACMG/AMP criteria review

Criteria shown when status is available

All criteria require review: For research and educational purposes only.

Criterion	Status	Rationale	Evidence used
PVS1	Not met	NM_000251.3:c.1316_1318del is an in-frame deletion (p.Pro439del) in exon 8 of MSH2. The InSiGHT MSH2 VCEP v2.0.0 PVS1 criteria are restricted to nonsense/frameshift variants introducing a premature termination codon, large genomic alterations, canonical splice site variants, or mRNA-confirmed splicing aberrations. This in-frame deletion does not introduce a PTC, does not affect a canonical splice site, and no patient mRNA assay data is available. PVS1 is not applicable to this variant type under the VCEP framework.	cspec pvs1_variant_assessment pvs1_gene_context
PS1	N/A	PS1 applies to missense substitutions encoding the same amino acid change as an established pathogenic variant, or variants affecting the same non-canonical splice nucleotide. NM_000251.3:c.1316_1318del is an in-frame deletion, not a missense substitution or splice variant. Not applicable to this variant type.	cspec
PS2	Not assessed	No de novo occurrence data is available for NM_000251.3:c.1316_1318del. Without confirmed de novo observations with maternity and paternity confirmation, PS2 cannot be assessed.
PS3	Not assessed	No variant-specific functional assay data is available for NM_000251.3:c.1316_1318del. The InSiGHT VCEP functional assay documentation (Functional-assay-SVI-documentation-MMR.xlsx) lists calibrated assays validated for MMR gene missense, splice site, and synonymous variants, but no assay results are reported for this in-frame deletion. OncoKB lists this variant as 'Unknown Oncogenic Effect' with no curated functional evidence.	oncokb vcep_functional_assay_svi_documentation_mmr
PS4	N/A	The InSiGHT MSH2 VCEP v2.0.0 declares PS4 as not applicable. Per the VCEP: 'Due to the availability of tumor IHC data for variant classification (see PP4), PS4 has not been utilized for MMR variant classification using proband counting.'	cspec
PS5	Not assessed	PS5 is not defined in the InSiGHT MSH2 VCEP v2.0.0 criteria set. No evidence is available to support a generic PS5 assessment for this variant.
PM1	N/A	The InSiGHT MSH2 VCEP v2.0.0 declares PM1 as not applicable. Per the VCEP: 'There are no recognized mutational hot spots that could be used for classification purposes. While there are functional domains in the MMR genes, the distribution of pathogenic variants is generalized over all the domains.'	cspec
PM2	Met	NM_000251.3:c.1316_1318del is absent from gnomAD v2.1, gnomAD v4.1, and gnomAD-Canada v1.0. This meets the InSiGHT MSH2 VCEP v2.0.0 PM2_Supporting threshold of absent/extremely rare allele frequency <0.00002 (<1 in 50,000 alleles) in gnomAD v4.	gnomad_v2 gnomad_v4 gnomad_canada cspec
PM4	N/A	The InSiGHT MSH2 VCEP v2.0.0 declares PM4 as not applicable. Per the VCEP: 'Protein length change from an in-frame variant is not used due to lack of evidence.'	cspec
PM5	N/A	PM5 applies to missense changes at an amino acid residue where a different missense change has been classified as pathogenic. NM_000251.3:c.1316_1318del is an in-frame deletion (p.Pro439del), not a missense substitution. The PM5 candidate analysis confirmed that this variant class is not eligible for classic same-residue missense PM5.	cspec pm5_candidates
PM6	N/A	The InSiGHT MSH2 VCEP v2.0.0 declares PM6 as not applicable. Per the VCEP: PM6 is designated 'Not applicable' for this gene.	cspec
PP1	Not assessed	No co-segregation data is available for NM_000251.3:c.1316_1318del. Segregation analysis with Bayes Likelihood Ratio calculation would be required to apply PP1 at any strength level under the VCEP framework.
PP2	N/A	The InSiGHT MSH2 VCEP v2.0.0 declares PP2 as not applicable. Per the VCEP: 'Missense variant in a gene with low rate of benign missense changes does not apply.'	cspec
PP3	N/A	The InSiGHT MSH2 VCEP v2.0.0 PP3 rules apply to missense variants (HCI prior probability thresholds) or predicted splice defects at non-canonical splice nucleotides (SpliceAI delta score >=0.2). NM_000251.3:c.1316_1318del is an in-frame deletion, not a missense variant, and SpliceAI predicts no splicing impact (max delta = 0.01). The variant does not fall within any VCEP-defined PP3 evidence category.	cspec spliceai
PP4	Not assessed	No tumor MSI/IHC data is available for patients carrying NM_000251.3:c.1316_1318del. PP4 under the InSiGHT VCEP requires CRC/endometrial MSI-H tumors and/or loss of MMR protein expression consistent with the variant location. Without tumor phenotype data, PP4 cannot be assessed.
PP5	N/A	The InSiGHT MSH2 VCEP v2.0.0 declares PP5 as 'Not Applicable for this VCEP'. Per the VCEP: 'This criterion is not for use as recommended by the ClinGen Sequence Variant Interpretation VCEP Review Committee.'	cspec
BA1	Not met	BA1 requires gnomAD v4 Grpmax filtering allele frequency >=0.001 (0.1%). NM_000251.3:c.1316_1318del is absent from gnomAD v4.1, well below the BA1 threshold. BA1 is not met.	gnomad_v4 cspec
BS1	Not met	BS1 requires gnomAD v4 Grpmax filtering allele frequency >=0.0001 and <0.001 (0.01-0.1%). NM_000251.3:c.1316_1318del is absent from gnomAD v4.1, below the BS1 threshold. BS1 is not met.	gnomad_v4 cspec
BS2	Not assessed	No data is available on co-occurrence of NM_000251.3:c.1316_1318del in trans with a known pathogenic MSH2 variant. BS2 requires phase-confirmed co-occurrence in a patient with colorectal cancer after age 45 (or other LS cancer above median onset age) without CMMRD features.
BS3	Not assessed	No variant-specific functional assay data demonstrating normal protein function is available for NM_000251.3:c.1316_1318del. No calibrated functional assay results with functional odds for pathogenicity <=0.48 (BS3_Supporting) or <=0.05 (BS3) have been reported for this variant.	vcep_functional_assay_svi_documentation_mmr
BS4	Not assessed	No segregation data is available to evaluate lack of co-segregation with disease. BS4 requires pedigree data with combined Bayes Likelihood Ratio calculation showing lack of co-segregation.
BP1	N/A	The InSiGHT MSH2 VCEP v2.0.0 declares BP1 as not applicable. Per the VCEP: 'Missense variant in a gene where only loss of function causes disease is not applicable.'	cspec
BP2	N/A	The InSiGHT MSH2 VCEP v2.0.0 declares BP2 as not applicable. Per the VCEP: 'BS2 is used instead.'	cspec
BP3	N/A	The InSiGHT MSH2 VCEP v2.0.0 declares BP3 as not applicable. Per the VCEP: 'In-frame deletions/insertions in a repetitive region without a known function is not used.'	cspec
BP4	N/A	The InSiGHT MSH2 VCEP v2.0.0 BP4 rules apply to missense variants (HCI prior probability <0.11) or intronic/synonymous variants (SpliceAI delta score <=0.1). NM_000251.3:c.1316_1318del is an in-frame deletion, not a missense, intronic, or synonymous variant. The variant does not fall within any VCEP-defined BP4 evidence category.	cspec spliceai
BP5	Not assessed	No data is available on the presence of an alternate molecular basis for disease in patients carrying NM_000251.3:c.1316_1318del. BP5 requires evidence of an alternate cause (e.g., BRAF V600E, MLH1 methylation, or another pathogenic variant explaining the phenotype).
BP6	N/A	The InSiGHT MSH2 VCEP v2.0.0 declares BP6 as 'Not Applicable for this VCEP'. Per the VCEP: 'This criterion is not for use as recommended by the ClinGen Sequence Variant Interpretation VCEP Review Committee.'	cspec
BP7	N/A	BP7 applies to synonymous (silent) or intronic variants at or beyond -21/+7. NM_000251.3:c.1316_1318del is an in-frame deletion within exon 8, resulting in the deletion of proline at codon 439. This is neither a synonymous nor an intronic variant. BP7 is not applicable.	cspec
PM3	N/A	PM3 was designated for skip by the adjudication workflow. Not assessed in this evaluation.

Disclaimer: The content and results provided by LYFE Sciences are for research and educational purposes only and must not be used as a substitute for professional medical judgment, diagnosis, or treatment. Always consult a qualified healthcare professional before making any clinical decisions.