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MLH1c.307-1G>AUncertain significance
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Variant interpretation report

MLH1 c.307-1G>A, p.?

NM_000249.4:c.307-1G>A NP_000240.1:p.? View identifiers
Classification
Uncertain significance

Variant description:

No variant summary was recorded for this case.

Five-step scale from benign to pathogenic. This variant is uncertain. Select a step to read what it means.

Uncertain.The recorded classification is uncertain significance.

In plain language

Gene-level background from the recorded interpretation.

About MLH1

No gene-level summary was recorded for this case.

LYFE Sciences is an AI system, and it can make mistakes. Criteria may be applied incorrectly, sources may be misread, and a confident-looking classification can still be wrong. Double-check every criterion and its underlying evidence before relying on any call.
01The reasoning

How it was classified

The recorded framework is ClinGen MLH1 VCEP v2.0.0. The criteria and strengths shown below come from the saved assessment; this page does not recalculate the classification.

Recorded applied criteria

The applied criteria and their strengths are shown as assessed under the stated framework.

Pathogenic evidence criteria: 2 Benign evidence criteria: 0
Pathogenic criteria applied · 2
PVS1Very strong
PVS1 · very strong

NM_000249.4:c.307-1G>A disrupts the canonical splice acceptor of intron 3 (IVS3-1G>A). Under the InSiGHT VCEP v2.0.0, variants at IVS±1 or IVS±2 where exon skipping or cryptic splice site use disrupts the reading frame and is predicted to undergo NMD are assigned PVS1_Very_Strong. Skipping of exon 4 (91 bp) would cause a frameshift and premature termination codon predicted to trigger nonsense-mediated decay. SpliceAI supports a severe splicing defect with a max delta score of 0.99 (acceptor loss). PP3 is not applied per VCEP guidance for IVS±1/2 variants receiving PVS1.

PM2Supporting
PM2 · supporting

The variant is absent from gnomAD v4.1 (0 alleles in the population database). Under the InSiGHT VCEP v2.0.0, an allele frequency <0.00002 (<1 in 50,000 alleles) in gnomAD v4 qualifies for PM2_Supporting. The variant is also absent from gnomAD v2.1 and gnomAD-Canada.

Benign criteria applied · 0

No benign criterion marked as applied in the recorded assessment.

Recorded classification: Uncertain significance

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 was evaluated deterministically with applied criteria: PVS1 very strong, PM2 supporting; no rule matched the adjudicated criteria.

02The sources

Evidence at a glance

Evidence summaries and captured source records, where available. Missing entries should not be interpreted as negative findings.

SpliceAI score
0.990 maximum delta

Recorded SpliceAI maximum delta score: 0.990. Refer to the recorded PP3/BP4 rationale for interpretation.

No listed criterion applied SpliceAI ↗
ClinVar submissions
2 reported laboratory submissions

2 Likely pathogenic. ClinVar API review status: criteria provided, multiple submitters, no conflicts.

Context only ClinVar ↗
No screenshot for this evidence
Functional evidence
Not recorded

No standalone functional evidence summary is recorded in evidence_summary.functional.

No listed criterion applied OncoKB ↗
Somatic evidence
1 recorded samples

This variant has previously been reported in somatic cancers (COSMIC; COSV99212388, n = 1 times).

Context only COSMIC ↗
For specialists

Technical detail

ACMG/AMP criteria under ClinGen MLH1 VCEP v2.0.0, with the data and sources behind each one.

26 criteria with recorded statuses: 2 met · 12 not met · 0 not assessed · 12 not applicable. Open any row for the full reasoning, the rule and the evidence behind it.

Pathogenic
PVS1PS1PS2PS3PS4PM1PM2PM5PM6PP1PP2PP3PP4PP5PS5
Benign
BA1BS1BS2BS3BS4BP1BP2BP4BP5BP6BP7
Met Not met Not assessed Not applicable

NM_000249.4:c.307-1G>A is a canonical splice acceptor variant (IVS3-1G>A) in MLH1, predicted to cause exon 4 skipping, frameshift, and nonsense-mediated decay.

SpliceAI predicts a severe splicing defect with a max delta score of 0.99 (acceptor loss), consistent with disruption of the canonical splice acceptor.

The variant is absent from gnomAD v4.1, v2.1, and gnomAD-Canada, indicating it is extremely rare in the general population.

Under the InSiGHT VCEP v2.0.0 for MLH1, the variant qualifies for PVS1_Very_Strong (IVS±1 disrupting reading frame with predicted NMD) and PM2_Supporting (absent from gnomAD v4 with AF <0.00002).

The variant has been reported in ClinVar as Likely pathogenic by two clinical laboratories (ClinVar Variation ID: 1727263) and has been observed once in somatic cancers (COSMIC: COSV99212388).

No functional studies, co-segregation data, de novo observations, or tumor phenotype data are available for this specific variant in the reviewed literature.

Met · 2

PVS1 Very strongNM_000249.4:c.307-1G>A disrupts the canonical splice acceptor of intron 3 (IVS3-1G>A). Under the InSiGHT VCEP v2.0.0, variants at IVS±1 or IVS±2 where exon skipping or cryptic splice site use disrupts the reading frame and is predicted to undergo NMD are assigned PVS1_Very_Strong. Skipping of exon 4 (91 bp) would cause a frameshift and premature termination codon predicted to trigger nonsense-mediated decay. SpliceAI supports a severe splicing defect with a max delta score of 0.99 (acceptor loss). PP3 is not applied per VCEP guidance for IVS±1/2 variants receiving PVS1. Details ▾Hide ▴
Evidence considered
  • Canonical splice acceptor variant at IVS3-1 (c.307-1G>A)
  • SpliceAI delta score 0.99 predicts acceptor loss
  • Exon 4 skipping (91 bp) disrupts reading frame
  • predicted NMD
  • MLH1 loss-of-function is an established disease mechanism per InSiGHT VCEP
Sources
cspec ↗spliceai ↗pvs1_variant_assessmentpvs1_gene_context
PM2 SupportingThe variant is absent from gnomAD v4.1 (0 alleles in the population database). Under the InSiGHT VCEP v2.0.0, an allele frequency <0.00002 (<1 in 50,000 alleles) in gnomAD v4 qualifies for PM2_Supporting. The variant is also absent from gnomAD v2.1 and gnomAD-Canada. Details ▾Hide ▴
Evidence considered
  • Absent from gnomAD v4.1 (AF = 0.0
  • meets <0.00002 threshold)
  • Absent from gnomAD v2.1
  • Absent from gnomAD-Canada v1.0
Sources
gnomad_v4 ↗gnomad_v2 ↗gnomad_canada ↗cspec ↗

Not met · 12 · evaluated, threshold not reached

PS2 No de novo observations have been reported for this variant. No publications or database entries document confirmed de novo occurrence with maternity and paternity confirmed. Details ▾Hide ▴
Still missing
  • No de novo data available
PS3 No variant-specific functional data were identified. The five publications associated with this case are clinical practice guidelines and policy statements that do not report experimental functional assays for NM_000249.4:c.307-1G>A. The VCEP functional assay documentation spreadsheet does not list this variant in calibrated assays. Details ▾Hide ▴
Still missing
  • No functional assay data available for this variant
PP1 No co-segregation data have been reported for this variant. No publications describe pedigree analysis or Bayes likelihood ratio calculations for NM_000249.4:c.307-1G>A. Details ▾Hide ▴
Still missing
  • No co-segregation data available
PP4 No tumor MSI/IHC phenotype data have been reported for patients carrying this variant. PP4 requires MSI-H tumor results and/or loss of MMR protein expression consistent with the variant location. No such data are available in the case record. Details ▾Hide ▴
Still missing
  • No tumor phenotype data (MSI/IHC) available
BA1 BA1 requires gnomAD v4 Grpmax filtering allele frequency ≥0.001 (0.1%). The variant is absent from gnomAD v4.1 and all other population databases. Threshold not met. Details ▾Hide ▴
Evidence considered
  • Absent from gnomAD v4.1 (AF = 0.0
  • far below 0.001 threshold)
Sources
gnomad_v4 ↗cspec ↗
BS1 BS1 requires gnomAD v4 allele frequency ≥0.0001 and <0.001 (0.01-0.1%). The variant is absent from gnomAD v4.1. Threshold not met. Details ▾Hide ▴
Evidence considered
  • Absent from gnomAD v4.1 (AF = 0.0
  • below 0.0001 threshold)
Sources
gnomad_v4 ↗cspec ↗
BS2 No evidence of co-occurrence in trans with a known pathogenic MLH1 variant in a patient without CMMRD features. No such data are available. Details ▾Hide ▴
Still missing
  • No trans co-occurrence data available
BS3 No functional studies demonstrating a benign effect for this variant have been identified. The five publications reviewed are clinical practice guidelines that do not contain experimental functional data. Details ▾Hide ▴
Still missing
  • No functional data demonstrating normal splicing or protein function
BS4 No lack-of-segregation data have been reported. No pedigrees demonstrating absence of co-segregation with disease are available. Details ▾Hide ▴
Still missing
  • No segregation data available
BP4 BP4_Supporting requires HCI prior probability <0.11 for missense variants, or SpliceAI delta score ≤0.1 for intronic/synonymous variants. This variant is intronic with SpliceAI max delta 0.99, far exceeding the 0.1 threshold. HCI prior is not available as this is not a missense variant. Both criteria for BP4 are not met. Details ▾Hide ▴
Evidence considered
  • SpliceAI max delta 0.99 (does not meet ≤0.1 threshold)
  • HCI prior not applicable (splice variant
  • not missense)
Sources
spliceai ↗cspec ↗
BP5 No tumor data showing MSS status or normal MMR protein expression have been reported for patients carrying this variant. BP5 requires multiple tumors with MSS and/or normal protein expression to provide benign evidence. Details ▾Hide ▴
Still missing
  • No tumor phenotype data available
BP7 BP7 applies to intronic variants at or beyond -21/+7 positions. The variant c.307-1G>A is at position -1 of intron 3, which is within the splice consensus region, not beyond it. The -1 position is a critical splice site nucleotide, not a deep intronic variant eligible for BP7. Details ▾Hide ▴
Evidence considered
  • Variant at IVS3-1: within canonical splice consensus
  • not beyond -21/+7
Sources
cspec ↗
Not applicable · 12· recorded as not applicable Show reasons ▾Hide reasons ▴
PS1 N/AVariant is a canonical splice site substitution, not a missense change. The PS1 rule for non-canonical splice nucleotides does not apply to canonical IVS±1/2 positions. Details ▾Hide ▴
Sources
cspec ↗
PS4 VCEPPS4 is explicitly marked 'Not Applicable' in the InSiGHT VCEP v2.0.0 specification for MLH1. Details ▾Hide ▴
Sources
cspec ↗
PM1 VCEPPM1 is explicitly marked 'Not Applicable' in the InSiGHT VCEP v2.0.0 specification for MLH1. Details ▾Hide ▴
Sources
cspec ↗
PM5 N/APM5 applies to missense changes at an amino acid residue where a different pathogenic missense change has been established. This is a canonical splice site variant (not a missense), and the pm5_candidates assessment confirms the variant class is not missense-like. PM5 is not applicable. Details ▾Hide ▴
Sources
cspec ↗pm5_candidates
PM6 VCEPPM6 is explicitly marked 'Not Applicable' in the InSiGHT VCEP v2.0.0 specification for MLH1. Details ▾Hide ▴
Sources
cspec ↗
PP2 VCEPPP2 is explicitly marked 'Not Applicable' in the InSiGHT VCEP v2.0.0 specification. Additionally, this is a splice site variant, not a missense variant. Details ▾Hide ▴
Sources
cspec ↗
PP3 N/AThe InSiGHT VCEP v2.0.0 specifies that PP3 is not to be combined with PVS1 for IVS±1 or IVS±2 variants. Since this variant (c.307-1G>A, IVS3-1) receives PVS1_Very_Strong, PP3 is excluded per VCEP guidance. Additionally, the SpliceAI PP3 rule applies only to non-canonical splice nucleotides, and this is a canonical splice site. Details ▾Hide ▴
Evidence considered
  • SpliceAI max delta 0.99 (acceptor loss) confirms severe predicted splicing impact
  • PP3 excluded per VCEP rule: 'Not to be combined with PP3' for IVS±1/2 variants receiving PVS1
Sources
cspec ↗spliceai ↗
PP5 VCEPPP5 is explicitly marked 'Not Applicable for this VCEP' in the InSiGHT VCEP v2.0.0 specification for MLH1. Details ▾Hide ▴
Sources
cspec ↗
BP1 VCEPBP1 is explicitly marked 'Not Applicable' in the InSiGHT VCEP v2.0.0 specification for MLH1. Details ▾Hide ▴
Sources
cspec ↗
BP2 VCEPBP2 is explicitly marked 'Not Applicable' in the InSiGHT VCEP v2.0.0 specification for MLH1. Details ▾Hide ▴
Sources
cspec ↗
BP6 VCEPBP6 is explicitly marked 'Not Applicable for this VCEP' in the InSiGHT VCEP v2.0.0 specification for MLH1. Details ▾Hide ▴
Sources
cspec ↗
PS5 N/APS5 is not defined in the InSiGHT VCEP v2.0.0 specification for MLH1. Details ▾Hide ▴
Sources
cspec ↗

Identifiers

Gene
MLH1
Transcript
NM_000249.4
Coding (HGVS c.)
NM_000249.4:c.307-1G>A
Protein (HGVS p.)
NP_000240.1:p.?
GRCh38
chr3:37004400 G>A
GRCh37
chr3:37045891 G>A
ClinVar
1727263
COSMIC
COSV99212388

Gene diagram

Every interpreted variant in MLH1, mapped onto the exon structure of NM_000249.4. Select a row to find it on the plot.

MLH1NM_000249.4
Fetching transcript structure from UCSC…
gnomAD v4.1 Allele count data not recorded
gnomAD v2.1 Allele count data not recorded
gnomAD-Canada v1.0 Allele count data not recorded

Statements

gnomAD v4.1

Absent from gnomAD v4.1.

gnomAD v2.1

Absent from gnomAD v2.1.

gnomAD-Canada

Absent from gnomAD-Canada v1.0.

SpliceAI and Pangolin

SpliceAI acceptor lossat +1 bp
0.990
SpliceAI acceptor gainat +2 bp
0.850
SpliceAI donor lossat +74 bp
0.090
SpliceAI donor gainat +189 bp
0.100
Pangolin splice lossmagnitude shown
-0.870
Pangolin splice gain
0.520

Other predictors

REVEL
Not available
BayesDel
0.660

How the predictions were used

BP4 BP4_Supporting requires HCI prior probability <0.11 for missense variants, or SpliceAI delta score ≤0.1 for intronic/synonymous variants. This variant is intronic with SpliceAI max delta 0.99, far exceeding the 0.1 threshold. HCI prior is not available as this is not a missense variant. Both criteria for BP4 are not met. Details ▾Hide ▴
Evidence considered
  • SpliceAI max delta 0.99 (does not meet ≤0.1 threshold)
  • HCI prior not applicable (splice variant
  • not missense)
Sources
spliceai ↗cspec ↗
BP7 BP7 applies to intronic variants at or beyond -21/+7 positions. The variant c.307-1G>A is at position -1 of intron 3, which is within the splice consensus region, not beyond it. The -1 position is a critical splice site nucleotide, not a deep intronic variant eligible for BP7. Details ▾Hide ▴
Evidence considered
  • Variant at IVS3-1: within canonical splice consensus
  • not beyond -21/+7
Sources
cspec ↗
PP3 N/AThe InSiGHT VCEP v2.0.0 specifies that PP3 is not to be combined with PVS1 for IVS±1 or IVS±2 variants. Since this variant (c.307-1G>A, IVS3-1) receives PVS1_Very_Strong, PP3 is excluded per VCEP guidance. Additionally, the SpliceAI PP3 rule applies only to non-canonical splice nucleotides, and this is a canonical splice site. Details ▾Hide ▴
Evidence considered
  • SpliceAI max delta 0.99 (acceptor loss) confirms severe predicted splicing impact
  • PP3 excluded per VCEP rule: 'Not to be combined with PP3' for IVS±1/2 variants receiving PVS1
Sources
cspec ↗spliceai ↗

Statement

In silico

SpliceAI predicts possible splice impact for this variant (max delta score = 0.99). BayesDel score = 0.66.

5 paper records listed. No publication is explicitly linked to an applied criterion in the recorded metadata. None of the listed paper records explicitly indicates that the variant is named.

Recorded publications

  • 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.
    National Society of Genetic Counselors and Collaborative Group of the Americas on Inherited Colorectal Cancer joint practice guideline for Lynch syndrome evaluation. Discusses MMR genes including MLH1 at the gene level. NM_000249.4:c.307-1G>A was not identified in this paper.
    Does not name this variant
    PMID 22167527 ↗
  • Informing family members of individuals with Lynch syndrome: a guideline for clinical geneticists.
    Menko FH et al. · 2013
    Dutch Society for Clinical Genetics guideline on informing family members of individuals with Lynch syndrome. Addresses ethical and procedural aspects of family communication. NM_000249.4:c.307-1G>A was not identified in this paper.
    Does not name this variant
    PMID 23535968 ↗
  • ACMG recommendations for reporting of incidental findings in clinical exome and genome sequencing.
    Green RC et al. · 2013
    ACMG recommendations for reporting incidental findings in clinical exome and genome sequencing. Lists genes including MLH1 as medically actionable but does not discuss specific variants. NM_000249.4:c.307-1G>A was not identified in this paper.
    Does not name this variant
    PMID 23788249 ↗
  • ACMG policy statement: updated recommendations regarding analysis and reporting of secondary findings in clinical genome-scale sequencing.
    ACMG policy statement updating recommendations for secondary findings analysis and reporting in clinical genome-scale sequencing. Discusses the 56-gene list but does not reference specific variants. NM_000249.4:c.307-1G>A was not identified in this paper.
    Does not name this variant
    PMID 25356965 ↗
  • Hereditary colorectal cancer syndromes: American Society of Clinical Oncology Clinical Practice Guideline endorsement of the familial risk-colorectal cancer: European Society for Medical Oncology Clinical Practice Guidelines.
    Stoffel EM et al. · 2015
    ASCO endorsement of ESMO clinical practice guidelines for hereditary colorectal cancer syndromes. Reviews Lynch syndrome, FAP, AFAP, and MAP at the syndrome/gene level. NM_000249.4:c.307-1G>A was not identified in this paper.
    Does not name this variant
    PMID 25452455 ↗

Screenshots represent source records captured during evidence collection. Select one to view the recorded source content.

gnomAD v4.1 Captured gnomAD v4.1 source record Open source ↗
gnomAD v2.1 Captured gnomAD v2.1 source record Open source ↗
SpliceAI Lookup Recorded maximum delta 0.990 Open source ↗
ClinVar 2 Likely pathogenic Open source ↗
COSMIC Captured COSMIC source record Open source ↗
ClinGen CSpec Captured ClinGen CSpec source record Open source ↗

All source links

Statements for reports

The evidence statements recorded by the interpretation pipeline. They have not been reinterpreted by the page.

gnomAD v4.1

Absent from gnomAD v4.1.

gnomAD v2.1

Absent from gnomAD v2.1.

gnomAD-Canada

Absent from gnomAD-Canada v1.0.

ClinVar

This variant has been reported in ClinVar as Likely pathogenic (2 clinical laboratories). (ClinVarID = 1727263)

In silico

SpliceAI predicts possible splice impact for this variant (max delta score = 0.99). BayesDel score = 0.66.

Somatic

This variant has previously been reported in somatic cancers (COSMIC; COSV99212388, n = 1 times).