Variant classification summary

NM_000251.3:c.211+9C>A

MSH2 · NP_000242.1:p.? · NM_000251.3

GRCh37: chr2:47630550 C>A · GRCh38: chr2:47403411 C>A

Gene: MSH2 Transcript: NM_000251.3

Final call

Likely Benign

PM2 supporting BP4 supporting benign BP7 supporting benign

Variant details

Gene

MSH2

Transcript

NM_000251.3

Protein

NP_000242.1:p.?

gnomAD AF

5.035595364734467e-06 (v4.1)

ClinVar

Likely benign

OncoKB

Classification rationale

Interpretation summary

Generated evidence synthesis

1

This variant is an intronic substitution at c.211+9 in MSH2, located beyond the +7 splice boundary, meeting BP7 (supporting benign).

2

SpliceAI predicts no splicing impact (max delta = 0.00), meeting BP4 (supporting benign) for intronic variants under the InSiGHT MSH2 VCEP (Walker et al. 2023).

3

This variant is present at extremely low frequency in gnomAD v4.1 (overall AF = 5.04 × 10⁻⁶, 8/1,588,690 alleles, 0 homozygotes), meeting PM2 at supporting strength under the InSiGHT MSH2 VCEP threshold of <0.00002.

4

The grpmax filtering allele frequency in gnomAD v4.1 is 8.99 × 10⁻⁵ (0.009%), which is below the BS1 threshold (≥ 0.0001) and the BA1 threshold (≥ 0.001); therefore BS1 and BA1 are not met.

5

PVS1 is not applicable — this is an intronic variant at +9, not a null variant or canonical splice site variant under the InSiGHT MSH2 VCEP PVS1 decision tree.

6

No tumor MSI/IHC, co-segregation, de novo, functional assay, or case-control data are available for this variant. No publications specifically report NM_000251.3:c.211+9C>A.

7

Under the InSiGHT MSH2 VCEP v2.0.0 combining rules, two supporting benign criteria (BP4, BP7) meet Rule 19 (≥ 2 Benign Supporting → Likely Benign). One pathogenic supporting criterion (PM2) is also present but does not trigger a VCEP-defined conflict with benign supporting evidence.

Final determination: Rule19 in the Richards et.al., 2015 - Combining rules v2.0.0 criteria-combination framework is satisfied by the adjudicated criteria, so the variant is classified as Likely Benign.

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	N/A	Intronic variant at c.211+9 position; does not fall into any PVS1 bucket under the InSiGHT MSH2 VCEP v2.0.0 framework (not a null variant, not at IVS±1/2, and no mRNA assay demonstrating splicing aberration).	cspec spliceai
PS1	Not met	No known pathogenic variant at the same non-canonical splice nucleotide (c.211+9) in MSH2. SpliceAI delta score of 0.00 would not meet the 'similar or worse splicing prediction' requirement even if a comparator existed.	cspec spliceai
PS2	Not met	No de novo reports available for NM_000251.3:c.211+9C>A. No publications describe a de novo occurrence of this variant with confirmed parentage.
PS3	Not met	No functional assay data available for this intronic variant. Under the InSiGHT MSH2 VCEP, PS3 for intronic variants requires calibrated functional assay data or laboratory mRNA aberration studies with NMD inhibition; none have been performed for this variant.	cspec spliceai
PS4	N/A	Criterion not applicable for this VCEP per the InSiGHT MSH2 specification v2.0.0.	cspec
PS5	N/A	Skipped — not in the assessment list for this case.
PM1	N/A	Criterion not applicable for this VCEP per the InSiGHT MSH2 specification v2.0.0.	cspec
PM2	Met	This variant is present at extremely low frequency in gnomAD v4.1 (overall allele frequency = 5.04 × 10⁻⁶; 8/1,588,690 alleles; 0 homozygotes), which is below the InSiGHT MSH2 VCEP threshold of <0.00002 (<1 in 50,000 alleles). Highest subpopulation frequency is in East Asian (AF = 0.000182; 8/43,960).	gnomad_v4
PM5	N/A	Intronic variant at c.211+9; PM5 requires a missense change at an amino acid residue with an established pathogenic missense comparator. This variant does not alter the amino acid sequence.	cspec
PM6	N/A	Criterion not applicable for this VCEP per the InSiGHT MSH2 specification v2.0.0.	cspec
PP1	Not met	No co-segregation data available for this variant. No family studies or pedigree analyses reporting segregation of NM_000251.3:c.211+9C>A with disease have been identified.
PP2	N/A	Criterion not applicable for this VCEP per the InSiGHT MSH2 specification v2.0.0.	cspec
PP3	Not met	For intronic variants, the InSiGHT MSH2 VCEP PP3 requires a SpliceAI delta score ≥ 0.2 for non-canonical splice nucleotides (Supporting strength). SpliceAI predicts no splicing impact for this variant (max delta = 0.00). HCI prior is not applicable as this is not a missense substitution.	cspec spliceai
PP4	Not met	No tumor MSI or immunohistochemistry data available for this variant. PP4 under the InSiGHT MSH2 VCEP requires CRC/endometrial tumor MSI-H status and/or loss of MMR protein expression consistent with the variant gene; no such clinical data have been reported.	cspec
PP5	N/A	Criterion not applicable for this VCEP per the InSiGHT MSH2 specification v2.0.0.	cspec
BA1	Not met	gnomAD v4.1 grpmax filtering allele frequency is 8.99 × 10⁻⁵ (0.009%), which is below the InSiGHT MSH2 VCEP BA1 threshold of ≥ 0.001 (≥ 0.1%).	gnomad_v4 cspec
BS1	Not met	gnomAD v4.1 grpmax filtering allele frequency is 8.99 × 10⁻⁵ (0.009%), which is below the InSiGHT MSH2 VCEP BS1 threshold of ≥ 0.0001 (0.01%).	gnomad_v4 cspec
BS2	Not met	No evidence of this variant occurring in trans with a known pathogenic MSH2 variant in a patient with colorectal cancer after age 45 and no CMMRD features.
BS3	Not met	No laboratory functional assay data available confirming absence of mRNA aberration or proficient MMR function for this specific intronic variant. The InSiGHT MSH2 VCEP BS3 for intronic variants requires laboratory assays conducted with NMD inhibition; SpliceAI computational predictions alone do not satisfy this criterion.	cspec spliceai
BS4	Not met	No lack-of-segregation data available. No pedigrees reporting absence of co-segregation of NM_000251.3:c.211+9C>A with disease.
BP1	N/A	Criterion not applicable for this VCEP per the InSiGHT MSH2 specification v2.0.0.	cspec
BP2	N/A	Criterion not applicable for this VCEP per the InSiGHT MSH2 specification v2.0.0 (BS2 is used instead).	cspec
BP3	N/A	Skipped — trivially not applicable (in-frame deletion/insertion criterion, variant is a substitution).
BP4	Met	SpliceAI predicts no splicing impact for this intronic variant (max delta score = 0.00 ≤ 0.1), meeting the InSiGHT MSH2 VCEP BP4 rule for intronic and synonymous variants as per Walker et al. 2023.	cspec spliceai
BP5	Not met	No tumor data available to assess MSS status, MMR protein expression, BRAF V600E, or MLH1 methylation. BP5 under the InSiGHT MSH2 VCEP requires tumor phenotype data inconsistent with the gene demonstrating genetic variation.
BP6	N/A	Criterion not for use as recommended by the ClinGen Sequence Variant Interpretation VCEP Review Committee per the InSiGHT MSH2 specification v2.0.0.	cspec
BP7	Met	This variant is intronic at position c.211+9, which is beyond +7 from the 3' end of exon 1, meeting the InSiGHT MSH2 VCEP BP7 rule for intronic variants at or beyond the -21/+7 boundaries. This variant may satisfy both BP7 and BP4.	cspec

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