3-37002998-A-T

Position:

• chr3-37002998-A-T

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_Strong BP6_Very_Strong BA1

The NM_000249.4(MLH1):​c.307-1403A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.151 in 152,172 control chromosomes in the GnomAD database, including 2,388 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★★).

• Frequency: Genomes: 𝑓 0.15 (2388 hom., cov: 32)
• Consequence: MLH1 NM_000249.4 intron
• Clinical Significance: Benign reviewed by expert panel B:2
• Conservation: PhyloP100: 0.0930

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=-0.74).
• BP6: Variant 3-37002998-A-T is Benign according to our data. Variant chr3-37002998-A-T is described in ClinVar as [Benign]. Clinvar id is 90152.Status of the report is reviewed_by_expert_panel, 3 stars. Variant chr3-37002998-A-T is described in Lovd as [Benign].
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.302 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MLH1	NM_000249.4	c.307-1403A>T		intron_variant		ENST00000231790.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MLH1	ENST00000231790.8	c.307-1403A>T		intron_variant		1	NM_000249.4	P1

Frequencies

GnomAD3 genomes AF: 0.151 AC: 23005 AN: 152054 Hom.: 2390 Cov.: 32

Gnomad AFR AF: 0.0346

Gnomad AMI AF: 0.174

Gnomad AMR AF: 0.161

Gnomad ASJ AF: 0.0983

Gnomad EAS AF: 0.315

Gnomad SAS AF: 0.302

Gnomad FIN AF: 0.264

Gnomad MID AF: 0.0759

Gnomad NFE AF: 0.183

Gnomad OTH AF: 0.132

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.151 AC: 23014 AN: 152172 Hom.: 2388 Cov.: 32 AF XY: 0.156 AC XY: 11592 AN XY: 74386

Gnomad4 AFR AF: 0.0346

Gnomad4 AMR AF: 0.161

Gnomad4 ASJ AF: 0.0983

Gnomad4 EAS AF: 0.315

Gnomad4 SAS AF: 0.303

Gnomad4 FIN AF: 0.264

Gnomad4 NFE AF: 0.183

Gnomad4 OTH AF: 0.135

Alfa AF: 0.162 Hom.: 343

Bravo AF: 0.135

Asia WGS AF: 0.277 AC: 961 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: reviewed by expert panel

Submissions by phenotype

Lynch syndrome Benign:1

Benign, reviewed by expert panel

research

International Society for Gastrointestinal Hereditary Tumours (InSiGHT)

Sep 05, 2013

MAF >1% -

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Jun 15, 2019

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.74
CADD	Benign	12
DANN	Benign	0.87

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: rs1540354; hg19: chr3-37044489;