NM_000249.4:c.222T>C is a synonymous variant (p.Asp74=) in exon 3 of MLH1. SpliceAI predicts no splicing impact (max delta score 0.03), satisfying BP4_Supporting under InSiGHT MLH1 VCEP v2.0.0 rules for synonymous variants.1 The variant is located within the -21 exonic splice region (c.222 in exon 3, acceptor c.208), satisfying BP7_Supporting.2 An RNA splicing assay performed by a clinical diagnostic laboratory indicates this variant does not significantly alter splicing, consistent with a benign functional effect (BS3_Supporting).3 The variant is present in gnomAD v4.1 at a low frequency (37/1,595,534 alleles; AF=2.32e-05) that exceeds the VCEP PM2_Supporting threshold of <0.00002, therefore PM2 is not met. The frequency does not reach BS1 or BA1 thresholds.4 The variant has been reported in ClinVar as Likely benign by six clinical laboratories (ClinVar ID 237333).5 No evidence of pathogenicity was identified: PVS1, PS1, and PM5 are not applicable (synonymous); PS2/PM6, PP1, PP4, BS2, BS4, and BP5 lack data; PS3, PP3, BA1, and BS1 are not met.6
MLH1
Final classification
Likely Benign
MLH1 c.222T>C · p.Asp74=
MLH1
NM_000249.4:c.222T>C is a synonymous variant (p.Asp74=) in exon 3 of MLH1.
ClinGen InSiGHT Hereditary Colorectal Cancer/Polyposis Expert Panel Specifications to the ACMG/AMP Variant Interpretation Guidelines for MLH1 Version 2.0.0 v2.0.0 criteria-combination framework: matched Rule19 (Benign.Supporting >=2) with applied criteria: BS3 supporting, BP4 supporting, BP7 supporting; maps to Likely Benign.
Classification rationale
BS3BP4BP7
Likely Benign
MLH1 c.222T>C
BS3 + BP4 + BP7
→
Likely Benign
Gene diagram
· NM_000249.4 · variants mapped to exon structure
MLH1
NM_000249.4
Fetching transcript structure from UCSC…
Applied criteria · 3 met · select any tile
Met
Not met
Not assessed
N/A
Strength
very strong
supporting
Pathogenic evidence
PVS
PS
PM
PP
Benign evidence
BA
BS
BP
—
—
—
Rationale
Select a criterion.
Sources
Evidence used
Gaps remaining
Rule
—
Research & evidence
Population frequency · supports benign
gnomAD v4.1
gnomAD v2.1
Population frequency
Overall AF
37 / 1,595,534
0.0023%
Highest · European (non-Finnish)
0.0032%
Homozygotes
0
grpmax FAF
0.0023%
Allele frequency by ancestry — gnomAD v4.1
observed in 1 of 9 groups
| Ancestry | Allele count | Frequency | Homozygotes |
|---|---|---|---|
| European (non-Finnish) | 37 / 1,163,262 | 0.0032% | 0 |
| Admixed American | 0 / 59,960 | — | — |
| European (Finnish) | 0 / 64,000 | — | — |
| Amish | 0 / 912 | — | — |
| East Asian | 0 / 44,732 | — | — |
| Middle Eastern | 0 / 6,058 | — | — |
| South Asian | 0 / 90,680 | — | — |
| Ashkenazi Jewish | 0 / 29,474 | — | — |
| African/African American | 0 / 74,548 | — | — |
“
This variant is present in gnomAD v4.1 (AF= 2.31897e-05; MAF= 0.00232%, 37/1595534 alleles, homozygotes = 0) and has highest observed frequency in the European (non-Finnish) population (AF= 3.18071e-05; MAF= 0.00318%, 37/1163262 alleles, homozygotes = 0); grpmax FAF= 2.347e-05.
Overall AF
2 / 251,356
0.0008%
Highest · European (non-Finnish)
0.0018%
Homozygotes
0
grpmax FAF
0.00029%
Allele frequency by ancestry — gnomAD v2.1
observed in 1 of 8 groups
| Ancestry | Allele count | Frequency | Homozygotes |
|---|---|---|---|
| European (non-Finnish) | 2 / 113,678 | 0.0018% | 0 |
| African/African American | 0 / 16,252 | — | — |
| Admixed American | 0 / 34,576 | — | — |
| Ashkenazi Jewish | 0 / 10,080 | — | — |
| East Asian | 0 / 18,394 | — | — |
| European (Finnish) | 0 / 21,644 | — | — |
| Remaining individuals | 0 / 6,130 | — | — |
| South Asian | 0 / 30,602 | — | — |
“
This variant is present in gnomAD v2.1 (AF= 7.95684e-06; MAF= 0.00080%, 2/251356 alleles, homozygotes = 0) and has highest observed frequency in the European (non-Finnish) population (AF= 1.75936e-05; MAF= 0.00176%, 2/113678 alleles, homozygotes = 0); grpmax FAF= 2.92e-06.
“
This variant is absent from gnomAD-Canada.
ClinVar
This variant has been reported in ClinVar as Likely benign (6 clinical laboratories) and as Uncertain significance (1 clinical laboratory) and as Benign (1 clinical laboratory). (ClinVarID = 237333)
In silico
SpliceAI predicts no significant splice impact for this variant (max delta score = 0.03). REVEL score = 0.035.
Functional
Unknown Oncogenic Effect
OncoKB identified curated literature and non-variant-specific oncogenicity context for review; listed oncogenicity label: Unknown Oncogenic Effect.
COSMIC
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.
Literature · 23 PMIDs triaged · 8 high-priority
23papers screened
Papers triaged by theme: functional/splicing/segregation/case_observation. high_priority_papers include abstract snippets. Use these to support PS3/BS3/PS4/PP1/PP3/PP5.
25070057 ↗
segregation
Guidelines on genetic evaluation and management of Lynch syndrome: a consensus statement by the US Multi-society Task Force on colorectal cancer.
The Multi-Society Task Force, in collaboration with invited experts, developed guidelines to assist health care providers with the appropriate provision of genetic testing and management of patients at risk for and affected with Lynch syndrome as follows: Figure 1 provides a colorectal cancer risk assessment tool to screen individuals in the office or endoscopy setting; Figure 2 illustrates a stra
BS4PP1PP5PS4
25645574 ↗
splicing rna
ACG clinical guideline: Genetic testing and management of hereditary gastrointestinal cancer syndromes.
This guideline presents recommendations for the management of patients with hereditary gastrointestinal cancer syndromes. The initial assessment is the collection of a family history of cancers and premalignant gastrointestinal conditions and should provide enough information to develop a preliminary determination of the risk of a familial predisposition to cancer. Age at diagnosis and lineage (ma
BP7PP3PP5PS4PVS1
25741868 ↗
functional
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.
The American College of Medical Genetics and Genomics (ACMG) previously developed guidance for the interpretation of sequence variants.(1) In the past decade, sequencing technology has evolved rapidly with the advent of high-throughput next-generation sequencing. By adopting and leveraging next-generation sequencing, clinical laboratories are now performing an ever-increasing catalogue of genetic
BS3PS3PS4
26467025 ↗
functional
A Standardized DNA Variant Scoring System for Pathogenicity Assessments in Mendelian Disorders.
We developed a rules-based scoring system to classify DNA variants into five categories including pathogenic, likely pathogenic, variant of uncertain significance (VUS), likely benign, and benign. Over 16,500 pathogenicity assessments on 11,894 variants from 338 genes were analyzed for pathogenicity based on prediction tools, population frequency, co-occurrence, segregation, and functional studies
BS3PS3PS4
11598466 ↗
case observation
Practice parameters for the identification and testing of patients at risk for dominantly inherited colorectal cancer--supporting documentation.
PP5PS4
20065170 ↗
case observation
American Society of Clinical Oncology policy statement update: genetic and genomic testing for cancer susceptibility.
PP5PS4
22167527 ↗
case observation
Identification of individuals at risk for Lynch syndrome using targeted evaluations and genetic testing: National Society of Genetic Counselors and the Collaborative Group of the Americas on Inherited Colorectal Cancer joint practice guideline.
Identifying individuals who have Lynch syndrome (LS) involves a complex diagnostic work up that includes taking a detailed family history and a combination of various genetic and immunohistochemical tests. The National Society of Genetic Counselors (NSGC) and the Collaborative Group of the Americas on Inherited Colorectal Cancer (CGA-ICC) have come together to publish this clinical practice testin
PP5PS4
28492532 ↗
background review
Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria.
PS3PS4
Sources & reference links