3-36993541-C-T

Variant names:

• chr3-36993541-C-T
• rs104894994
• NM_000249.4:c.-7C>T

Variant summary

Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4 BP6 BS2

The NM_000249.4(MLH1):​c.-7C>T variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000576 in 1,614,000 control chromosomes in the GnomAD database, including 3 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).

• Frequency:
  • Genomes: 𝑓 0.00089 (0 hom., cov: 33)
  • Exomes 𝑓: 0.00054 (3 hom.)
• Consequence: MLH1 NM_000249.4 5_prime_UTR
• Clinical Significance: Conflicting classifications of pathogenicity criteria provided, conflicting classifications U:2 B:12 O:2
• Conservation: PhyloP100: 0.185

Genes affected

MLH1 (HGNC:7127): (mutL homolog 1) The protein encoded by this gene can heterodimerize with mismatch repair endonuclease PMS2 to form MutL alpha, part of the DNA mismatch repair system. When MutL alpha is bound by MutS beta and some accessory proteins, the PMS2 subunit of MutL alpha introduces a single-strand break near DNA mismatches, providing an entry point for exonuclease degradation. The encoded protein is also involved in DNA damage signaling and can heterodimerize with DNA mismatch repair protein MLH3 to form MutL gamma, which is involved in meiosis. This gene was identified as a locus frequently mutated in hereditary nonpolyposis colon cancer (HNPCC). [provided by RefSeq, Aug 2017]

ACMG classification

Verdict is Likely_benign. Variant got -6 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.18).
• BP6: Variant 3-36993541-C-T is Benign according to our data. Variant chr3-36993541-C-T is described in ClinVar as [Conflicting_classifications_of_pathogenicity]. Clinvar id is 89599.We mark this variant Likely_benign, oryginal submissions are: {Likely_benign=4, Benign=6, Uncertain_significance=2, not_provided=2}. Variant chr3-36993541-C-T is described in Lovd as [Likely_benign].
• BS2: High Homozygotes in GnomAdExome4 at 3 AD,AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MLH1	NM_000249.4	c.-7C>T		5_prime_UTR_variant	Exon 1 of 19	ENST00000231790.8	NP_000240.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MLH1	ENST00000231790	c.-7C>T		5_prime_UTR_variant	Exon 1 of 19	1	NM_000249.4	ENSP00000231790.3

Frequencies

GnomAD3 genomes AF: 0.000893 AC: 136 AN: 152260 Hom.: 0 Cov.: 33

Gnomad AFR AF: 0.0000241

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.000131

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.000192

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00988

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.000382

Gnomad OTH AF: 0.000478

GnomAD3 exomes AF: 0.00126 AC: 317 AN: 251462 Hom.: 3 AF XY: 0.00119 AC XY: 162 AN XY: 135916

Gnomad AFR exome AF: 0.00

Gnomad AMR exome AF: 0.0000867

Gnomad ASJ exome AF: 0.00

Gnomad EAS exome AF: 0.00

Gnomad SAS exome AF: 0.0000653

Gnomad FIN exome AF: 0.00809

Gnomad NFE exome AF: 0.00105

Gnomad OTH exome AF: 0.00277

GnomAD4 exome AF: 0.000543 AC: 794 AN: 1461622 Hom.: 3 Cov.: 31 AF XY: 0.000524 AC XY: 381 AN XY: 727132

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.0000671

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.0000348

Gnomad4 FIN exome AF: 0.00792

Gnomad4 NFE exome AF: 0.000270

Gnomad4 OTH exome AF: 0.00108

GnomAD4 genome AF: 0.000893 AC: 136 AN: 152378 Hom.: 0 Cov.: 33 AF XY: 0.00127 AC XY: 95 AN XY: 74514

Gnomad4 AFR AF: 0.0000240

Gnomad4 AMR AF: 0.000131

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.000193

Gnomad4 SAS AF: 0.00

Gnomad4 FIN AF: 0.00988

Gnomad4 NFE AF: 0.000382

Gnomad4 OTH AF: 0.000473

Alfa AF: 0.000168 Hom.: 0

Bravo AF: 0.000128

Asia WGS AF: 0.00289 AC: 10 AN: 3478

EpiCase AF: 0.000109

EpiControl AF: 0.0000593

ClinVar

Significance: Conflicting classifications of pathogenicity

Submissions summary: Uncertain:2 Benign:12 Other:2

Revision: criteria provided, conflicting classifications

Submissions by phenotype

not provided Uncertain:1 Benign:2 Other:2

Sep 02, 2022

Mayo Clinic Laboratories, Mayo Clinic

Significance: Uncertain significance

Review Status: criteria provided, single submitter

Collection Method: clinical testing

BS1 -

Dec 14, 2020

Quest Diagnostics Nichols Institute San Juan Capistrano

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Sep 02, 2020

GeneDx

Significance: Likely benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

Has no predicted effect on splicing and the nucleotide is not conserved across species; Published functional studies are inconclusive: when studied with c.-28A>G, not associated with MLH1 promoter methylation and conflicting results regarding impact on MLH1 expression (Hesson 2015, Morak 2018); Observed with c.-28A>G and in isolation in individuals with MLH1-associated and other cancers (Fredriksson 2006, Hesson 2015, Lagerstedt-Robinson 2016, Morak 2018, Jarhelle 2019, Nikitin 2020); This variant is associated with the following publications: (PMID: 26888055, 25762362, 24689082, 32547938, 16963262, 27601186, 29472279, 31882575) -

-

GenomeConnect, ClinGen

Significance: not provided

Review Status: no classification provided

Collection Method: phenotyping only

Variant interpreted as Uncertain significance and reported on 09-02-2020 by Lab or GTR ID 506138. GenomeConnect assertions are reported exactly as they appear on the patient-provided report from the testing laboratory. GenomeConnect staff make no attempt to reinterpret the clinical significance of the variant. -

-

Harris Lab, University of Minnesota

Significance: not provided

Review Status: no classification provided

Collection Method: literature only

- -

not specified Uncertain:1 Benign:3

Mar 04, 2025

Center for Genomic Medicine, Rigshospitalet, Copenhagen University Hospital

Significance: Likely benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Mar 05, 2020

Women's Health and Genetics/Laboratory Corporation of America, LabCorp

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

Variant summary: MLH1 c.-7C>T is located in the untranslated mRNA region upstream of the initiation codon. The variant allele was found at a frequency of 0.0013 in 251462 control chromosomes in the gnomAD database, including 3 homozygotes. The observed variant frequency is approximately 1.8- fold the estimated maximal expected allele frequency for a pathogenic variant in MLH1 causing Hereditary Non-Polyposis Colon Cancer phenotype (0.00071), strongly suggesting that the variant is benign. c.-7C>T has been reported in the literature in individuals affected with Hereditary Non-Polyposis Colon Cancer (examples-Hesson_2015, Lagerstedt-Robinson_2016). The variant has also been detected in individuals reported to have hereditary prostate cancer (Fredriksson_2006) and non-HNPCC cancer phenotypes (Morak_2018). These reports do not provide unequivocal conclusions about association of the variant with Hereditary Non-Polyposis Colon Cancer. One publication reports experimental evidence suggesting that the variant results in a 50% reduction in MLH1 expression,however, does not allow convincing conclusions about the variant effect (Hesson_2015). Three other clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar after 2014 without evidence for independent evaluation. They cited the variant as benign (n=2) and uncertain significance (n=1). Based on the evidence outlined above, the variant was classified as benign. -

Jul 09, 2019

Genetic Services Laboratory, University of Chicago

Significance: Uncertain significance

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Aug 10, 2020

Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

The c.-7C>T variant in MLH1 is classified as benign because it has been identified in 0.80% (202/25118, 2 homozygotes) of Finnish chromosomes by gnomAD (http://gnomad.broadinstitute.org). Identified in 2 families with this variant and suggested a partial loss of MLH1 expression (Hesson 2015 PMID:25762362). ACMG/AMP Criteria applied: BA1. -

Hereditary cancer-predisposing syndrome Benign:3

Oct 02, 2020

Sema4, Sema4

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: curation

- -

Sep 20, 2018

Ambry Genetics

Significance: Likely benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. -

Nov 17, 2015

Color Diagnostics, LLC DBA Color Health

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Colorectal cancer, hereditary nonpolyposis, type 2 Benign:1

Nov 15, 2024

Myriad Genetics, Inc.

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

This variant is considered benign. This variant has been observed at a population frequency that is significantly greater than expected given the associated disease prevalence and penetrance. This variant is strongly associated with less severe personal and family histories of cancer, typical for individuals without pathogenic variants in this gene [PMID: 27363726]. -

Carcinoma of colon Benign:1

-

Department of Pathology and Laboratory Medicine, Sinai Health System

Significance: Likely benign

Review Status: no assertion criteria provided

Collection Method: clinical testing

The MLH1 c.-7C>T variant was identified in 2 of 980 proband chromosomes (frequency: 0.002) from individuals or families with Lynch syndrome (Fredriksson 2006, Lagerstedt-Robinson 2016). The variant was also identified in dbSNP (ID: rs104894994) as "With Uncertain significance allele", ClinVar (classified as benign by Invitae; as uncertain significance by GeneDx, InSight and Mayo Clinic), and in LOVD 3.0 (11x). The variant was not identified in UMD-LSDB database. The variant was identified in control databases in 357 of 277232 chromosomes (3 homozygous) at a frequency of 0.001, increasing the likelihood this could be a low frequency benign variant (Genome Aggregation Database Feb 27, 2017). The variant was observed in the following populations: Other in 13 of 6464 chromosomes (freq: 0.002), Latino in 3 of 34418 chromosomes (freq: 0.00009), European in 132 of 126720 chromosomes (freq: 0.001), Finnish in 207 of 25788 chromosomes (freq: 0.008), and South Asian in 2 of 30782 chromosomes (freq: 0.00007), but not in the African, Ashkenazi Jewish, or East Asian populations. One study by identified that the c.-7C>T variant was associated with partial constitutional loss of MLH1 expression and suggests it is the most likely cause of predisposition to CRC with MMR deficiency and loss of MLH1 (Hesson 2015). However, the same study confirmed the variant co-segregated on the same chromosome with MLH1 c.1164del (predicted to cause a frameshift) in one of the tested probands, increasing the likelihood that the variant does not have clinical significance (Hesson 2015). In summary, based on the above information, the clinical significance of this variant cannot be determined with certainty at this time although we would lean towards a more benign role for this variant. This variant is classified as likely benign. -

Breast and/or ovarian cancer Benign:1

Aug 09, 2021

CHEO Genetics Diagnostic Laboratory, Children's Hospital of Eastern Ontario

Significance: Likely benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Hereditary nonpolyposis colorectal neoplasms Benign:1

Dec 02, 2024

Labcorp Genetics (formerly Invitae), Labcorp

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.18
CADD	Benign	19
DANN	Uncertain	0.99
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.0

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs104894994; hg19: chr3-37035032;