chr3-36993537-C-T

Variant names:

• chr3-36993537-C-T
• rs776898290
• NM_000249.4:c.-11C>T

Variant summary

Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BP4_Strong

The NM_000249.4(MLH1):​c.-11C>T variant causes a 5 prime UTR premature start codon gain change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000198 in 1,614,010 control chromosomes in the GnomAD database, with no homozygous occurrence. 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 0.0000066 (0 hom., cov: 33)
  • Exomes 𝑓: 0.000021 (0 hom.)
• Consequence: MLH1 NM_000249.4 5_prime_UTR_premature_start_codon_gain
• Clinical Significance: Conflicting classifications of pathogenicity criteria provided, conflicting classifications U:9 B:1
• Conservation: PhyloP100: 0.0530

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 -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.63).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MLH1	NM_000249.4	c.-11C>T		5_prime_UTR_premature_start_codon_gain_variant	Exon 1 of 19	ENST00000231790.8	NP_000240.1
MLH1	NM_000249.4	c.-11C>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.-11C>T		5_prime_UTR_premature_start_codon_gain_variant	Exon 1 of 19	1	NM_000249.4	ENSP00000231790.3
MLH1	ENST00000231790	c.-11C>T		5_prime_UTR_variant	Exon 1 of 19	1	NM_000249.4	ENSP00000231790.3

Frequencies

GnomAD3 genomes AF: 0.00000657 AC: 1 AN: 152276 Hom.: 0 Cov.: 33

Gnomad AFR AF: 0.00

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0000654

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00

Gnomad OTH AF: 0.00

GnomAD3 exomes AF: 0.0000119 AC: 3 AN: 251472 Hom.: 0 AF XY: 0.0000147 AC XY: 2 AN XY: 135920

Gnomad AFR exome AF: 0.00

Gnomad AMR exome AF: 0.00

Gnomad ASJ exome AF: 0.00

Gnomad EAS exome AF: 0.00

Gnomad SAS exome AF: 0.0000327

Gnomad FIN exome AF: 0.00

Gnomad NFE exome AF: 0.0000176

Gnomad OTH exome AF: 0.00

GnomAD4 exome AF: 0.0000212 AC: 31 AN: 1461734 Hom.: 0 Cov.: 31 AF XY: 0.0000220 AC XY: 16 AN XY: 727182

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.0000252

Gnomad4 SAS exome AF: 0.0000232

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.0000243

Gnomad4 OTH exome AF: 0.0000166

GnomAD4 genome AF: 0.00000657 AC: 1 AN: 152276 Hom.: 0 Cov.: 33 AF XY: 0.0000134 AC XY: 1 AN XY: 74404

Gnomad4 AFR AF: 0.00

Gnomad4 AMR AF: 0.0000654

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.00

Gnomad4 OTH AF: 0.00

ClinVar

Significance: Conflicting classifications of pathogenicity

Submissions summary: Uncertain:9 Benign:1

Revision: criteria provided, conflicting classifications

Submissions by phenotype

not provided Uncertain:2

May 10, 2018

GeneDx

Significance: Uncertain significance

Review Status: criteria provided, single submitter

Collection Method: clinical testing

This variant is denoted MLH1 c.-11C>T, and describes a nucleotide substitution 11 base pairs upstream of the MLH1 ATG translational start site in the 5' untranslated region (UTR). The surrounding sequence, with the base that is substituted in brackets, is TCTT[C/T]TGGC. This variant has been observed in at least three individuals with colon cancer whose tumors demonstrated microsatellite instability (MSI-H) and/or absence of MLH1 expression by immunohistochemistry (IHC). While one of these individuals' tumors was also positive for MLH1 promoter hypermethylation, the other two were not (Hampel 2008. Ward 2013). MLH1 c.-11C>T has been reported to reduce promoter activity compared to wild type (Ward 2013). MLH1 c.-11C>T was not observed in approximately 6,500 individuals of European and African American ancestry in the NHLBI Exome Sequencing Project, suggesting it is not a common benign variant in these populations. The cytosine (C) nucleotide that is altered is not conserved. This variant does not appear to affect the start codon or the Kozak translational consensus sequence, and is not predicted to affect splicing. However, in the absence of RNA or functional studies, the actual effect of this variant is unknown. Based on currently available evidence, it is unclear whether MLH1 c.-11C>T is pathogenic or benign. We consider it to be a variant of uncertain significance. -

Feb 24, 2017

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

Significance: Uncertain significance

Review Status: criteria provided, single submitter

Collection Method: clinical testing

Variant summary: The MLH1 c.-11C>T variant involves the alteration of a non-conserved nucleotide located in the 5'UTR. Mutation Taster predicts a benign outcome for this variant. This variant is absent in 121940 control chromosomes including broad and large population from ExAC. This variant has previously been reported in two colon cancer patients, one with both MSI and MLHI IHC negative tumor, the other with either MSI or MLH1 IHC negative tumor, consistent with disease-causing outcome of the variant (Ward_2013). This report also performed functional studies in which c.-11C>T showed a significant reduction in promoter activity as compared with the wild-type promoter sequence (~49% and ~62% of wild-type activity in HCT116 and HEK293 cells, respectively). Taken together, this variant is currently classified as VUS-possibly pathogenic. -

Colorectal cancer, hereditary nonpolyposis, type 2 Uncertain:1 Benign:1

Dec 05, 2023

Baylor Genetics

Significance: Uncertain significance

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Nov 15, 2024

Myriad Genetics, Inc.

Significance: Likely benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

This variant is considered likely benign. 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]. -

not specified Uncertain:1

Mar 04, 2025

Center for Genomic Medicine, Rigshospitalet, Copenhagen University Hospital

Significance: Uncertain significance

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Inherited MMR deficiency (Lynch syndrome) Uncertain:1

May 14, 2024

Genomics and Molecular Medicine Service, East Genomic Laboratory Hub, NHS Genomic Medicine Service

Significance: Uncertain significance

Review Status: criteria provided, single submitter

Collection Method: clinical testing

PP4_Moderate -

Muir-Torré syndrome;C1333991:Colorectal cancer, hereditary nonpolyposis, type 2;C5399763:Mismatch repair cancer syndrome 1 Uncertain:1

Aug 03, 2021

Center for Genomics, Ann and Robert H. Lurie Children's Hospital of Chicago

Significance: Uncertain significance

Review Status: criteria provided, single submitter

Collection Method: clinical testing

MLH1 NM_000249.2 c.-11C>T: This variant has been reported in the literature in at least three individuals with colorectal cancer; these individuals had tumor screening that showed absence of MLH1 on IHC and/or microsatellite instability (MSI) (Hampel 2008 PMID:18809606, Ward 2013 PMID:22878509). This variant is present in 0.006% (1/15290) of Latino alleles in the Genome Aggregation Database (https://gnomad.broadinstitute.org/variant/3-36993537-C-T?dataset=gnomad_r3). Please note, disease causing variants may be present in control databases at low frequencies, reflective of the general population, carrier status, and/or variable expressivity. This variant is present in ClinVar (Variation ID:421030). Evolutionary conservation and computational predictive tools for this variant are limited or unavailable. This variant represents a single nucleotide change in the upstream 5' untranslated region (UTR) of the gene. In vitro functional studies showed a significant reduction in promotor activity with this variant compared to the wild-type promotor sequence (Ward 2013 PMID:22878509). However, these studies may not accurately represent in vivo biological function. In summary, data on this variant is insufficient for disease classification. Therefore, the clinical significance of this variant is uncertain. -

Hereditary nonpolyposis colorectal neoplasms Uncertain:1

Dec 26, 2024

Labcorp Genetics (formerly Invitae), Labcorp

Significance: Uncertain significance

Review Status: criteria provided, single submitter

Collection Method: clinical testing

This variant occurs in a non-coding region of the MLH1 gene. It does not change the encoded amino acid sequence of the MLH1 protein. This variant is present in population databases (rs776898290, gnomAD 0.003%). This variant has been observed in individual(s) with colorectal cancer (PMID: 18809606, 22878509). ClinVar contains an entry for this variant (Variation ID: 421030). Algorithms developed to predict the effect of variants on gene product structure and function are not available or were not evaluated for this variant. Experimental studies have shown that this variant affects MLH1 function (PMID: 22878509). In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. -

Malignant tumor of breast Uncertain:1

-

Department of Pathology and Laboratory Medicine, Sinai Health System

Significance: Uncertain significance

Review Status: no assertion criteria provided

Collection Method: clinical testing

The MLH1 c.-11C>T variant was identified in 2 of 832 proband chromosomes (frequency: 0.002) from individuals with Lynch Syndrome, at least one of whom had abnormal IHC results (Ward 2013). The variant was identified in dbSNP (rs776898290) as “with uncertain significance allele and ClinVar (classified as uncertain significance by Color, GeneDx and Integrated Genetics). The variant was not identified in UMD-LSDB. The variant was identified in control databases in 3 of 246,260 chromosomes at a frequency of 0.00001 (Genome Aggregation Database Feb 27, 2017). The variant was observed in the following populations: European in 2 of 111,710 chromosomes (freq: 0.00002) and South Asian in 1 of 30,782 chromosomes (freq: 0.00003); it was not observed in the African, Other, Latino, Ashkenazi Jewish, East Asian or Finnish populations. The c.-11C>T variant is located upstream of the Kozak sequence and the effect of this variant on promoter activity cannot be predicted with in silico tools. However, the variant demonstrated a significant reduction in promoter activity in a luciferase assay (Ward 2013). In summary, based on the above information, the clinical significance of this variant cannot be determined with certainty at this time. This variant is classified as a variant of uncertain significance. -

Hereditary cancer-predisposing syndrome Uncertain:1

Aug 10, 2023

Color Diagnostics, LLC DBA Color Health

Significance: Uncertain significance

Review Status: criteria provided, single submitter

Collection Method: clinical testing

This variant is located in the 5' untranslated region of the MLH1 gene. This variant has been reported in individuals affected with Lynch syndrome and colorectal cancer (PMID: 8809606, 22878509, 37433431, 37270516). Additionally, the variant has been reported to reduce promoter activity (PMID: 22878509). This variant has been identified in 3/251472 chromosomes in the general population by the Genome Aggregation Database (gnomAD). Although there is a suspicion that this variant may be associated with disease, additional clinical and functional studies are necessary to determine the role of this variant in disease conclusively. Therefore, this variant is classified as a Variant of Uncertain Significance. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.63
CADD	Benign	11
DANN	Benign	0.91

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: rs776898290; hg19: chr3-37035028; COSMIC: COSV99212448; COSMIC: COSV99212448;