rs35908749

chr3-37014456-G-A

Variant summary

Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_Moderate BP6_Very_Strong BP7 BS1

The NM_000249.4(MLH1):c.702G>A(p.Glu234=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000453 in 1,604,218 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★★).

• Frequency:
  • Genomes: 𝑓 0.00042 (0 hom., cov: 32)
  • Exomes 𝑓: 0.00046 (1 hom.)
• Consequence: MLH1 NM_000249.4 synonymous
• Clinical Significance: Likely benign reviewed by expert panel U:1 B:18
• Conservation: PhyloP100: 0.629

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 -15 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.42).
• BP6: Variant 3-37014456-G-A is Benign according to our data. Variant chr3-37014456-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 36558.Status of the report is reviewed_by_expert_panel, 3 stars. Variant chr3-37014456-G-A is described in Lovd as [Likely_benign].
• BP7: Synonymous conserved (PhyloP=0.629 with no splicing effect.
• BS1: Variant frequency is greater than expected in population amr. gnomad4_exome allele frequency = 0.000456 (662/1451944) while in subpopulation AMR AF= 0.000805 (36/44696). AF 95% confidence interval is 0.000598. There are 1 homozygotes in gnomad4_exome. There are 324 alleles in male gnomad4_exome subpopulation. Median coverage is 28. This position pass quality control queck.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MLH1	NM_000249.4	c.702G>A	p.Glu234=	synonymous_variant	9/19	ENST00000231790.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MLH1	ENST00000231790.8	c.702G>A	p.Glu234=	synonymous_variant	9/19	1	NM_000249.4	P1

Frequencies

GnomAD3 genomes AF: 0.000421 AC: 64 AN: 152156 Hom.: 0 Cov.: 32

Gnomad AFR AF: 0.000121

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.000589

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.000622

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.000647

Gnomad OTH AF: 0.00144

GnomAD3 exomes AF: 0.000426 AC: 107 AN: 251146 Hom.: 0 AF XY: 0.000398 AC XY: 54 AN XY: 135750

Gnomad AFR exome AF: 0.000124

Gnomad AMR exome AF: 0.000839

Gnomad ASJ exome AF: 0.00

Gnomad EAS exome AF: 0.00

Gnomad SAS exome AF: 0.000327

Gnomad FIN exome AF: 0.0000462

Gnomad NFE exome AF: 0.000546

Gnomad OTH exome AF: 0.000490

GnomAD4 exome AF: 0.000456 AC: 662 AN: 1451944 Hom.: 1 Cov.: 28 AF XY: 0.000448 AC XY: 324 AN XY: 723078

Gnomad4 AFR exome AF: 0.0000901

Gnomad4 AMR exome AF: 0.000805

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.000395

Gnomad4 FIN exome AF: 0.0000187

Gnomad4 NFE exome AF: 0.000505

Gnomad4 OTH exome AF: 0.000466

GnomAD4 genome AF: 0.000420 AC: 64 AN: 152274 Hom.: 0 Cov.: 32 AF XY: 0.000430 AC XY: 32 AN XY: 74444

Gnomad4 AFR AF: 0.000120

Gnomad4 AMR AF: 0.000588

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.000622

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.000647

Gnomad4 OTH AF: 0.00142

Alfa AF: 0.000403 Hom.: 0

Bravo AF: 0.000506

EpiCase AF: 0.000654

EpiControl AF: 0.000652

ClinVar

Significance: Likely benign

Submissions summary: Uncertain:1 Benign:18

Revision: reviewed by expert panel

Submissions by phenotype

Hereditary cancer-predisposing syndrome Benign:5

Likely benign, criteria provided, single submitter	clinical testing	Color Diagnostics, LLC DBA Color Health	Apr 01, 2015	- -
Benign, criteria provided, single submitter	clinical testing	Institute for Biomarker Research, Medical Diagnostic Laboratories, L.L.C.	Nov 06, 2023	- -
Likely benign, no assertion criteria provided	clinical testing	True Health Diagnostics	Oct 04, 2018	- -
Likely benign, criteria provided, single submitter	clinical testing	Ambry Genetics	Aug 01, 2014	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. -
Benign, criteria provided, single submitter	curation	Sema4, Sema4	Oct 20, 2020	- -

not provided Benign:4

Likely benign, criteria provided, single submitter	clinical testing	CeGaT Center for Human Genetics Tuebingen	Apr 01, 2024	MLH1: BP4, BP7 -
Likely benign, criteria provided, single submitter	clinical testing	Women's Health and Genetics/Laboratory Corporation of America, LabCorp	May 03, 2016	Variant summary: This synonymous variant is located 25 nts downstream of intron-exon junction in coding region. 3/5 splice-site tools predict the variant not to have effect on splicing and two independent functional studies showed that this variant does not have effect on normal splicing (Borras et al 2012 and Thompson et al 2013). This variant has been reported in multiple HNPCC patients mostly of European origin, albeit some of them did not fulfilling Amsterdam criteria for HNPCC diagnosis. In one patient, another variant that could explain the phenotype was also detected. The variant was found at a frequency of 0.0392% in the general population (47/119650 chromosomes), clustered mainly in the population of European origin with no homozygous occurrence. This frequency in general population is lower than the maximal expected allele frequency (0.07%) for pathogenic MLH1 variant. Lastly, reputable databases and diagnostic centers classify the variant as likely benign/benign/neutral. Taken together, this variant has been classified as likely benign. -
Likely benign, no assertion criteria provided	clinical testing	Clinical Genetics, Academic Medical Center	-	- -
Likely benign, no assertion criteria provided	clinical testing	Joint Genome Diagnostic Labs from Nijmegen and Maastricht, Radboudumc and MUMC+	-	- -

not specified Benign:3

Benign, criteria provided, single submitter	clinical testing	GeneDx	Jan 23, 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. -
Likely benign, criteria provided, single submitter	clinical testing	Center for Genomic Medicine, Rigshospitalet, Copenhagen University Hospital	Aug 15, 2023	- -
Likely benign, no assertion criteria provided	clinical testing	Mayo Clinic Laboratories, Mayo Clinic	-	- -

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

Uncertain significance, 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. However, the evidence from the literature, in combination with allele frequency data from public databases where available, was not sufficient to rule this variant in or out of causing disease. Therefore, this variant is classified as a variant of unknown significance. -
Likely benign, criteria provided, single submitter	clinical testing	Mendelics	May 28, 2019	- -

Lynch syndrome Benign:2

Likely benign, criteria provided, single submitter	clinical testing	All of Us Research Program, National Institutes of Health	Feb 05, 2024	- -
Likely benign, reviewed by expert panel	research	International Society for Gastrointestinal Hereditary Tumours (InSiGHT)	Sep 05, 2013	Synonymous substitution with no splicing aberration, treated with NMD inhibitor -

Breast and/or ovarian cancer Benign:1

Likely benign, criteria provided, single submitter

clinical testing

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

Jun 24, 2021

- -

Hereditary nonpolyposis colorectal neoplasms Benign:1

Benign, criteria provided, single submitter

clinical testing

Invitae

Jan 31, 2024

- -

Malignant tumor of breast Benign:1

Likely benign, no assertion criteria provided

clinical testing

Department of Pathology and Laboratory Medicine, Sinai Health System

-

The MLH1 p.Glu234Glu variant was identified in 5 of 1752 proband chromosomes (frequency: 0.003) from individuals or families with colon cancer or hereditary non-polyposis colorectal cancer and was not identified in 604 control chromosomes from healthy individuals (Borras 2012, Curia 1999, Grabowski 2004, Caldes 2002). The variant was also identified the following databases: dbSNP (ID: rs35908749) as “With Likely benign allele”, ClinVar (classified as benign 2x by GeneDx and Invitae; and classified as likely benign 4x by InSiGHT, Ambry Genetics, Color Genomics, Laboratory Corporation of America), Clinvitae (classified 2x as benign by GeneDx and Invitae; 4x as likely benign by Ambry Genetics, Color Genomics, InSiGHT, Laboratory Corporation of America), UMD-LSDB (observed 8x), Insight Colon Cancer Gene Variant Database (5x pathogenicity unknown, 1x probably no pathogenicity), Mismatch Repair Genes Variant Database, Insight Hereditary Tumors Database (6 references, all classified as “probably does not affect function”). The variant was not identified in COGR, COSMIC, MutDB, or the Zhejiang Colon Cancer Databases. The variant was identified in control databases in 110 of 276966 chromosomes at a frequency of 0.0004 in the following populations: Latino in 27 of 34398 chromosomes (freq. 0.0008); European non-Finnish in 67 of 126622 chromosomes (freq. 0.0005); South Asian in 10 of 30766 chromosomes (freq. 0.0003); population listed as Other in 2 of 6458 chromosomes (freq. 0.0003); and African in 3 of 23948 chromosomes (freq. 0.0001) increasing the likelihood this could be a low frequency benign variant (Genome Aggregation Consortium Feb 27, 2017). This variant was identified in a patient with endometrial cancer whose family meets Amsterdam criteria and was negative for MLH1 by IHC, however this variant did not affect mRNA processing or stability and the authors conclude that the variant is likely neutral (Borras 2012). Additionally, this patient was found to have two other MLH1 missense variants which resulted in exon 9 skipping and a truncated protein. This variant was also observed in a patient with colon cancer and resulted in a modest germline transcript unbalance in a primer extension assay (Curia 1999). The p.Glu234Glu variant is not expected to have clinical significance because it does not result in a change of amino acid. Three of five in silico or computational prediction software programs (SpliceSiteFinder, MaxEntScan, NNSPLICE, GeneSplicer, HumanSpliceFinder) predict a greater than 10% difference in splicing however this information is not very predictive of pathogenicity. 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. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.42
Cadd	Benign	6.5
Dann	Benign	0.64

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: rs35908749; hg19: chr3-37055947;