rs193922367

chr3-37025629-T-A

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_Strong BP6_Very_Strong BS1 BS2

The NM_000249.4(MLH1):c.1039-8T>A variant causes a splice region, splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00777 in 1,225,154 control chromosomes in the GnomAD database, including 47 homozygotes. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Benign (★★★).

• Frequency:
  • Genomes: 𝑓 0.011 (7 hom., cov: 25)
  • Exomes 𝑓: 0.0073 (40 hom.)
• Consequence: MLH1 NM_000249.4 splice_region, splice_polypyrimidine_tract, intron
• Scores: Splicing: ADA: 0.003561
• Clinical Significance: Benign reviewed by expert panel U:1 B:23
• Conservation: PhyloP100: -0.155

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 Benign. Variant got -20 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BP6: Variant 3-37025629-T-A is Benign according to our data. Variant chr3-37025629-T-A is described in ClinVar as [Benign]. Clinvar id is 36539.Status of the report is reviewed_by_expert_panel, 3 stars. Variant chr3-37025629-T-A is described in Lovd as [Benign]. Variant chr3-37025629-T-A is described in Lovd as [Likely_benign].
• BS1: Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.0114 (1506/132268) while in subpopulation AFR AF= 0.0201 (661/32840). AF 95% confidence interval is 0.0189. There are 7 homozygotes in gnomad4. There are 666 alleles in male gnomad4 subpopulation. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd at 6 AD,AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MLH1	NM_000249.4	c.1039-8T>A		splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant		ENST00000231790.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MLH1	ENST00000231790.8	c.1039-8T>A		splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant		1	NM_000249.4	P1

Frequencies

GnomAD3 genomes AF: 0.0114 AC: 1502 AN: 132280 Hom.: 6 Cov.: 25

Gnomad AFR AF: 0.0200

Gnomad AMI AF: 0.00340

Gnomad AMR AF: 0.00566

Gnomad ASJ AF: 0.00764

Gnomad EAS AF: 0.00407

Gnomad SAS AF: 0.00292

Gnomad FIN AF: 0.00366

Gnomad MID AF: 0.00752

Gnomad NFE AF: 0.0106

Gnomad OTH AF: 0.00898

GnomAD3 exomes AF: 0.0257 AC: 3016 AN: 117468 Hom.: 56 AF XY: 0.0249 AC XY: 1683 AN XY: 67558

Gnomad AFR exome AF: 0.0868

Gnomad AMR exome AF: 0.0127

Gnomad ASJ exome AF: 0.00944

Gnomad EAS exome AF: 0.0215

Gnomad SAS exome AF: 0.00949

Gnomad FIN exome AF: 0.0168

Gnomad NFE exome AF: 0.0301

Gnomad OTH exome AF: 0.0273

GnomAD4 exome AF: 0.00733 AC: 8010 AN: 1092886 Hom.: 40 Cov.: 19 AF XY: 0.00753 AC XY: 4066 AN XY: 540322

Gnomad4 AFR exome AF: 0.0213

Gnomad4 AMR exome AF: 0.00691

Gnomad4 ASJ exome AF: 0.00486

Gnomad4 EAS exome AF: 0.00513

Gnomad4 SAS exome AF: 0.00526

Gnomad4 FIN exome AF: 0.0105

Gnomad4 NFE exome AF: 0.00707

Gnomad4 OTH exome AF: 0.00763

GnomAD4 genome AF: 0.0114 AC: 1506 AN: 132268 Hom.: 7 Cov.: 25 AF XY: 0.0104 AC XY: 666 AN XY: 64110

Gnomad4 AFR AF: 0.0201

Gnomad4 AMR AF: 0.00565

Gnomad4 ASJ AF: 0.00764

Gnomad4 EAS AF: 0.00409

Gnomad4 SAS AF: 0.00293

Gnomad4 FIN AF: 0.00366

Gnomad4 NFE AF: 0.0106

Gnomad4 OTH AF: 0.00891

Alfa AF: 0.0280 Hom.: 11

ClinVar

Significance: Benign

Submissions summary: Uncertain:1 Benign:23

Revision: reviewed by expert panel

Submissions by phenotype

not specified Benign:10

Benign, criteria provided, single submitter	clinical testing	ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories	Jul 06, 2018	- -
Benign, criteria provided, single submitter	clinical testing	GeneDx	Aug 27, 2014	This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. -
Benign, no assertion criteria provided	clinical testing	Mayo Clinic Laboratories, Mayo Clinic	-	- -
Benign, no assertion criteria provided	clinical testing	Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine	Oct 29, 2008	- -
Benign, no assertion criteria provided	clinical testing	Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center	-	- -
Benign, no assertion criteria provided	clinical testing	Genome Diagnostics Laboratory, Amsterdam University Medical Center	-	- -
Benign, no assertion criteria provided	clinical testing	Laboratory of Diagnostic Genome Analysis, Leiden University Medical Center (LUMC)	-	- -
Benign, no assertion criteria provided	clinical testing	Clinical Genetics Laboratory, Department of Pathology, Netherlands Cancer Institute	-	- -
Benign, no assertion criteria provided	clinical testing	Joint Genome Diagnostic Labs from Nijmegen and Maastricht, Radboudumc and MUMC+	-	- -
Benign, criteria provided, single submitter	clinical testing	Eurofins Ntd Llc (ga)	Jan 19, 2017	- -

Colorectal cancer, hereditary nonpolyposis, type 2 Uncertain:1 Benign:3

Uncertain significance, criteria provided, single submitter	clinical testing	Center for Human Genetics, Inc, Center for Human Genetics, Inc	Nov 01, 2016	- -
Likely benign, criteria provided, single submitter	clinical testing	Mendelics	May 28, 2019	- -
Benign, no assertion criteria provided	clinical testing	Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen	-	- -
Benign, criteria provided, single submitter	clinical testing	Illumina Laboratory Services, Illumina	Apr 27, 2017	This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). Publications were found based on this search. The evidence from the literature, in combination with allele frequency data from public databases where available, was sufficient to rule this variant out of causing disease. Therefore, this variant is classified as benign. -

Hereditary cancer-predisposing syndrome Benign:4

Benign, criteria provided, single submitter	clinical testing	Color Diagnostics, LLC DBA Color Health	Feb 18, 2015	- -
Benign, criteria provided, single submitter	clinical testing	Ambry Genetics	Nov 18, 2014	This alteration is classified as 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. -
Likely benign, no assertion criteria provided	clinical testing	True Health Diagnostics	Sep 28, 2017	- -
Benign, criteria provided, single submitter	curation	Sema4, Sema4	Mar 22, 2020	- -

Lynch syndrome 1 Benign:2

Benign, reviewed by expert panel	research	International Society for Gastrointestinal Hereditary Tumours (InSiGHT)	Apr 20, 2016	Reported 32 times by French labs. Splicing reporter minigene pCAS: normal splicing. Linkage disequilibrium with MLH1: c.1558+14G>A. Found in co-occurrence with MSH2 : c.1387_1661del (loss of exons 9 and 10). -
Benign, no assertion criteria provided	clinical testing	Pathway Genomics	Jul 24, 2014	- -

Breast and/or ovarian cancer Benign:1

Benign, criteria provided, single submitter

clinical testing

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

May 01, 2019

- -

Lynch syndrome Benign:1

Benign, no assertion criteria provided

clinical testing

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

Dec 22, 2011

- -

Hereditary nonpolyposis colorectal neoplasms Benign:1

Benign, criteria provided, single submitter

clinical testing

Invitae

Feb 01, 2024

- -

Endometrial carcinoma Benign:1

Benign, no assertion criteria provided

clinical testing

Department of Pathology and Laboratory Medicine, Sinai Health System

-

The MLH1 c.1039-8T>A variant was identified in 42 of 2222 proband chromosomes (frequency: 0.019) from individuals with Lynch syndrome or sporadic colorectal cancer; and was present in of 857 of 18938 control chromosomes (frequency: 0.045) from these studies (Arnold 2009, Mangold 2005, Pastrello 2011, Rouleau 2008, Thomsen 2013, Wang 1998). The variant is located in the 3' splice region but does not affect the invariant -1 and -2 positions; however, positions -3 and -5 to -12 are part of the splicing consensus sequence and variants involving these positions sometimes affect splicing. Two studies report the c.1039-8T>A variant at polymorphic frequencies in control individuals, increasing the likelihood that it does not have clinical importance (Arnold 2009, Thomsen 2013). In addition, statistical studies suggest that this variant had a decreased risk of HNPCC-related cancer and therefore had no effect or is likely non-pathogenic (Thomsen 2013, Pastrello 2011). In summary, based on the above information, this variant meets our lab's criteria to be classified as benign. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
Cadd	Benign	1.2
Dann	Benign	0.78

Splicing

Name	Calibrated prediction	Score	Prediction
dbscSNV1_ADA	Benign	0.0036
dbscSNV1_RF	Benign	0.034
SpliceAI score (max)		0.020		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: rs193922367; hg19: chr3-37067120; COSMIC: COSV104573003; COSMIC: COSV104573003;