rs369521379

Positions:

Variant summary

Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PP3_Moderate

The NM_000249.4(MLH1):c.453G>A(p.Thr151=) variant causes a splice region, synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000279 in 1,610,186 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 2/3 splice prediction tools predicting alterations to normal splicing. Variant has been reported in ClinVar as Uncertain significance (★★★). Synonymous variant affecting the same amino acid position (i.e. T151T) has been classified as Uncertain significance.

Frequency

Genomes: 𝑓 0.000059 ( 0 hom., cov: 32)

Exomes 𝑓: 0.000025 ( 0 hom. )

Consequence

MLH1
NM_000249.4 splice_region, synonymous

Scores

Splicing: ADA: 0.9998

Clinical Significance

Uncertain significance reviewed by expert panel U:16

Conservation

PhyloP100: 0.311

Variant links:

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]

MLH1 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 2 ACMG points.

PP3

Splicing scoreres supports a deletorius effect: Scorers claiming Pathogenic: dbscSNV1_ADA, dbscSNV1_RF. Scorers claiming Uncertain: max_spliceai. No scorers claiming Benign.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MLH1	NM_000249.4 linkuse as main transcript	c.453G>A	p.Thr151=	splice_region_variant, synonymous_variant	5/19	ENST00000231790.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MLH1	ENST00000231790.8 linkuse as main transcript	c.453G>A	p.Thr151=	splice_region_variant, synonymous_variant	5/19	1	NM_000249.4	P1	P40692-1

Frequencies

GnomAD3 genomes

AF:

0.0000592

AC:

AN:

152116

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.000145

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.000385

Gnomad SAS

AF:

0.00

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.0000147

Gnomad OTH

AF:

0.00

GnomAD3 exomes

AF:

0.00000796

AC:

AN:

251372

Hom.:

AF XY:

0.00

AC XY:

AN XY:

135868

show subpopulations

Gnomad AFR exome

AF:

0.00

Gnomad AMR exome

AF:

0.0000289

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:

0.00

Gnomad OTH exome

AF:

0.00

GnomAD4 exome

AF:

0.0000247

AC:

AN:

1458070

Hom.:

Cov.:

AF XY:

0.0000220

AC XY:

AN XY:

725652

show subpopulations

Gnomad4 AFR exome

AF:

0.0000599

Gnomad4 AMR exome

AF:

0.0000447

Gnomad4 ASJ exome

AF:

0.00

Gnomad4 EAS exome

AF:

0.000328

Gnomad4 SAS exome

AF:

0.00

Gnomad4 FIN exome

AF:

0.00

Gnomad4 NFE exome

AF:

0.0000153

Gnomad4 OTH exome

AF:

0.0000332

GnomAD4 genome

AF:

0.0000592

AC:

AN:

152116

Hom.:

Cov.:

AF XY:

0.0000538

AC XY:

AN XY:

74296

show subpopulations

Gnomad4 AFR

AF:

0.000145

Gnomad4 AMR

AF:

0.00

Gnomad4 ASJ

AF:

0.00

Gnomad4 EAS

AF:

0.000385

Gnomad4 SAS

AF:

0.00

Gnomad4 FIN

AF:

0.00

Gnomad4 NFE

AF:

0.0000147

Gnomad4 OTH

AF:

0.00

Alfa

AF:

0.0000435

Hom.:

Bravo

AF:

0.0000907

ClinVar

Significance: Uncertain significance

Submissions summary: Uncertain:16

Revision: reviewed by expert panel

LINK: link

Submissions by phenotype

not specified

Uncertain:3

Uncertain significance, criteria provided, single submitter	clinical testing	Women's Health and Genetics/Laboratory Corporation of America, LabCorp	Feb 06, 2024	Variant summary: MLH1 c.453G>A (p.Thr151Thr) alters a conserved nucleotide located close to a canonical splice site and therefore could affect mRNA splicing, leading to a significantly altered protein sequence. Several computational tools predict a significant impact on normal splicing: One predict the variant abolishes the canonical 5' splicing donor site. One predict the variant creates a 3' acceptor site. Three predict the variant weakens the canonical 5' splicing donor site. However, these predictions have yet to be confirmed by functional studies. The variant allele was found at a frequency of 8e-06 in 251372 control chromosomes. The available data on variant occurrences in the general population are insufficient to allow any conclusion about variant significance. c.453G>A has been reported in the literature in individuals affected with/undergoing testing for Hereditary Nonpolyposis Colorectal Cancer/Lynch syndrome or other cancers and also as a VUS in settings of multigene panel testing in individuals with colorectal cancer and Breast and/or ovarian cancer (example, Shirts_2016, Sunga_2017, Kiyozumi_2019, Molina-Zayas_2022). A large case-control study evaluating Biliary tract cancer reported the variant insignificantly distributed between cases and controls (Okawa_2023). These reports do not provide unequivocal conclusions about association of the variant with Hereditary Nonpolyposis Colorectal Cancer/Lynch syndrome. At-least one co-occurrence with another pathogenic variant has been observed at our laboratory (BRCA1 c.188T>A, p.Leu63Ter), providing supporting evidence for a benign role. To our knowledge, no experimental evidence demonstrating an impact on protein function has been reported. The following publications have been ascertained in the context of this evaluation (PMID: 31386297, 35451682, 36243179, 26845104, 28449805). ClinVar contains an entry for this variant (Variation ID: 90229). Based on the evidence outlined above, the variant was classified as uncertain significance. -
Uncertain significance, criteria provided, single submitter	clinical testing	Center for Genomic Medicine, Rigshospitalet, Copenhagen University Hospital	Jul 31, 2024	- -
Uncertain significance, criteria provided, single submitter	clinical testing	Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine	Feb 21, 2017	The p.Thr151Thr variant in MLH1 has been reported in one individual with colorec tal polyps and a family history of colorectal cancer (Shirts 2016). This variant has been identified in 1/16492 of South Asian chromosomes by the Exome Aggregat ion Consortium (ExAC, http://exac.broadinstitute.org; dbSNP rs369521379). Althou gh the p.Thr151Thr variant does not alter an amino acid residue, it is located i n the last base of the exon, which is part of the 5? splice region. Computationa l tools suggest some impact to splicing though this information is not predictiv e enough to determine pathogenicity. In contrast, this variant has been classifi ed as Likely Pathogenic on Sept 5, 2013 by the ClinGen-approved InSiGHT expert p anel (ClinVarSCV000106723.2), due a predicted splicing effect that has not been confirmed by published functional studies. In summary, the clinical significance of the p.Thr151Thr variant is uncertain. -

Colorectal cancer, hereditary nonpolyposis, type 2

Uncertain:3

Uncertain significance, criteria provided, single submitter	clinical testing	St. Jude Molecular Pathology, St. Jude Children's Research Hospital	Aug 19, 2021	The MLH1 c.453G>A (p.Thr151=) synonymous change has a maximum subpopulation frequency of 0.0040% in gnomAD v2.1.1 (https://gnomad.broadinstitute.org/variant/3-37048554-G-A). Algorithms that predict the impact of sequence changes on splicing indicate that this change may create or strengthen a splice site (PP3), but this prediction has not been confirmed by RNA studies. This variant has been reported in individuals with colorectal cancer and/or clinical features of Lynch syndrome (PMID: 26845104, 28449805, 33309985), individuals with other cancers (PMID: 31386297, 32634176), and in a tumor that demonstrated loss-of-heterozygosity of the wild-type allele (PMID: 29887214). It has also been reported in non-cancer controls (PMID: 33309985). In summary, this variant meets criteria to be classified as of uncertain significance based on the ACMG/AMP criteria: PP3. -
Uncertain significance, criteria provided, single submitter	clinical testing	Mendelics	Apr 20, 2020	- -
Uncertain significance, criteria provided, single submitter	clinical testing	Baylor Genetics	Jan 17, 2024	- -

not provided

Uncertain:3

Uncertain significance, criteria provided, single submitter	clinical testing	Quest Diagnostics Nichols Institute San Juan Capistrano	Sep 17, 2019	- -
Uncertain significance, criteria provided, single submitter	clinical testing	GeneDx	Aug 10, 2023	Not observed at significant frequency in large population cohorts (gnomAD); In silico analysis suggests this variant may impact gene splicing. In the absence of RNA/functional studies, the actual effect of this sequence change is unknown.; Observed in individuals with Lynch-related and other cancers as well as polyps, but also in cancer-free controls (Shirts et al., 2016; Sunga et al., 2017; Matejcic et al., 2020; Singh et al., 2020; Okawa et al., 2023); This variant is associated with the following publications: (PMID: 32832836, 28449805, 31386297, 12414824, 26845104, 30720243, 35451682, 36243179, 32634176, 33309985) -
Uncertain significance, criteria provided, single submitter	clinical testing	Eurofins Ntd Llc (ga)	Oct 24, 2016	- -

Hereditary cancer-predisposing syndrome

Uncertain:3

Uncertain significance, criteria provided, single submitter	curation	Sema4, Sema4	Sep 18, 2021	- -
Uncertain significance, criteria provided, single submitter	clinical testing	Ambry Genetics	Aug 16, 2023	The c.453G>A variant (also known as p.T151T) located in coding exon 5 of the MLH1 gene. This variant results from a G to A substitution at nucleotide position 453. This nucleotide substitution does not change the threonine at codon 151. However, this change occurs in the last base pair of exon 5 which makes it likely to have some effect on normal mRNA splicing. This alteration has been detected in numerous individuals who do not have a personal or family history that is consistent with or suggestive of hereditary nonpolyposis colorectal cancer (HNPCC)/Lynch syndrome (Ambry internal data). In one study, p.Thr151Thr was seen in 20/12503 unselected Japanese colorectal cancer patients and in 28/23705 controls (Fujita M et al. Clin Gastroenterol Hepatol, 2020 Dec). This alteration has been identified in an individual suspected of having Lynch syndrome, an individual with polyps, and a woman with endometrial cancer (Sunga AY et al. Cancer Genet, 2017 04;212-213:1-7; Shirts BH et al. Genet. Med., 2016 10;18:974-81; Singh AK et al. PLoS One, 2020 Jul;15:e0235613). This alteration was also detected in a study of 1,165 individuals with a history of colorectal cancer or colon polyps as well as 590 controls (Gordon AS et al. Am J Hum Genet, 2019 09;105:526-533). This nucleotide position is not well conserved in available vertebrate species. In silico splice site analysis predicts that this alteration may result in the creation or strengthening of a novel splice donor site. RNA studies have demonstrated an incomplete splice defect for this alteration resulting in a transcript predicted to lead to a protein with an in-frame insertion of 3 amino acids; however, the exact functional impact of the inserted amino acids is unknown at this time (Ambry internal data). Since supporting evidence is limited at this time, the clinical significance of this alteration remains unclear. -
Uncertain significance, criteria provided, single submitter	clinical testing	Color Diagnostics, LLC DBA Color Health	Dec 05, 2022	This synonymous variant does not change the amino acid sequence of the MLH1 protein but does change the last base of exon 5. Splice site prediction tools suggest that this variant may impact RNA splicing. However, this prediction has not been confirmed in published RNA studies. This variant has been reported in individuals affected with polyps (PMID: 26845104), lung cancer (PMID: 31386297), breast/ovarian cancer (PMID: 32068069), endometrial cancer (PMID: 32634176), and in a cohort of individuals affected with suspected Lynch syndrome (PMID: 28449805). However, case-control studies in Japan reported no association with colorectal (PMID: 33309985) or pancreatic cancer (PMID: 32980694). This variant has also been identified in 3/282760 chromosomes in the general population by the Genome Aggregation Database (gnomAD). The available evidence is insufficient to determine the role of this variant in disease conclusively. Therefore, this variant is classified as a Variant of Uncertain Significance. -

Breast and/or ovarian cancer

Uncertain:1

Uncertain significance, criteria provided, single submitter

clinical testing

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

Mar 03, 2021

- -

Lynch syndrome 1

Uncertain:1

Uncertain significance, reviewed by expert panel

curation

International Society for Gastrointestinal Hereditary Tumours (InSiGHT)

Jun 13, 2018

Criteria changed for variants in last base of exon therefore downgrade classification -

Lynch syndrome

Uncertain:1

Uncertain significance, criteria provided, single submitter

clinical testing

University of Washington Department of Laboratory Medicine, University of Washington

May 01, 2018

MLH1 NM_000249.3:c.453G>A has a 75.7% probability of pathogenicity based on combining prior probability from public data with a likelihood ratio of 0.16 to 1, generated from evidence of seeing this as a somatic mutation in a tumor with loss of heterozygosity at the MLH1 locus. See Shirts et al 2018, PMID 29887214. This was also reported in Shirts et al 2016, PMID 26845104 in an individual with a family history of colorectal cancer. -

Hereditary nonpolyposis colorectal neoplasms

Uncertain:1

Uncertain significance, criteria provided, single submitter

clinical testing

Invitae

Oct 25, 2022

This sequence change affects codon 151 of the MLH1 mRNA. It is a 'silent' change, meaning that it does not change the encoded amino acid sequence of the MLH1 protein. RNA analysis indicates that this variant induces altered splicing and likely results in the gain of 3 amino acid residue(s), but is expected to preserve the integrity of the reading-frame. This variant is present in population databases (rs369521379, gnomAD 0.004%). This variant has been observed in individual(s) with colon cancer and lung cancer (PMID: 26845104, 28449805, 31386297). ClinVar contains an entry for this variant (Variation ID: 90229). Variants that disrupt the consensus splice site are a relatively common cause of aberrant splicing (PMID: 17576681, 9536098). Studies have shown that this variant results in the activation of a cryptic splice site in intron 5 (Invitae). 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. -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.25

CADD

Uncertain

DANN

Benign

0.85

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

2.9

Splicing

Name

Calibrated prediction

Score

Prediction

dbscSNV1_ADA

Pathogenic

1.0

dbscSNV1_RF

Pathogenic

0.99

SpliceAI score (max)

0.31

Details are displayed if max score is > 0.2

DS_DG_spliceai

0.31

Position offset: 9

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over