7-116795968-G-A

Position:

chr7-116795968-G-A

Variant summary

Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1

The ENST00000397752.8(MET):c.4017G>A(p.Ala1339=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.435 in 1,613,922 control chromosomes in the GnomAD database, including 158,321 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★). Synonymous variant affecting the same amino acid position (i.e. A1339A) has been classified as Likely benign.

Frequency

Genomes: 𝑓 0.35 ( 11151 hom., cov: 32)

Exomes 𝑓: 0.44 ( 147170 hom. )

Consequence

MET
ENST00000397752.8 synonymous

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:14

Conservation

PhyloP100: -0.968

Variant links:

Genes affected

MET (HGNC:7029): (MET proto-oncogene, receptor tyrosine kinase) This gene encodes a member of the receptor tyrosine kinase family of proteins and the product of the proto-oncogene MET. The encoded preproprotein is proteolytically processed to generate alpha and beta subunits that are linked via disulfide bonds to form the mature receptor. Further processing of the beta subunit results in the formation of the M10 peptide, which has been shown to reduce lung fibrosis. Binding of its ligand, hepatocyte growth factor, induces dimerization and activation of the receptor, which plays a role in cellular survival, embryogenesis, and cellular migration and invasion. Mutations in this gene are associated with papillary renal cell carcinoma, hepatocellular carcinoma, and various head and neck cancers. Amplification and overexpression of this gene are also associated with multiple human cancers. [provided by RefSeq, May 2016]

MET links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -21 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.72).

BP6

Variant 7-116795968-G-A is Benign according to our data. Variant chr7-116795968-G-A is described in ClinVar as [Benign]. Clinvar id is 93575.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr7-116795968-G-A is described in Lovd as [Benign].

BP7

Synonymous conserved (PhyloP=-0.968 with no splicing effect.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.455 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein
MET	NM_000245.4 linkuse as main transcript	c.4017G>A	p.Ala1339=	synonymous_variant	21/21	ENST00000397752.8	NP_000236.2
MET	NM_001127500.3 linkuse as main transcript	c.4071G>A	p.Ala1357=	synonymous_variant	21/21		NP_001120972.1
MET	NM_001324402.2 linkuse as main transcript	c.2727G>A	p.Ala909=	synonymous_variant	20/20		NP_001311331.1
MET	XM_011516223.2 linkuse as main transcript	c.4074G>A	p.Ala1358=	synonymous_variant	22/22		XP_011514525.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MET	ENST00000397752.8 linkuse as main transcript	c.4017G>A	p.Ala1339=	synonymous_variant	21/21	1	NM_000245.4	ENSP00000380860	P3	P08581-1
MET	ENST00000318493.11 linkuse as main transcript	c.4071G>A	p.Ala1357=	synonymous_variant	21/21	1		ENSP00000317272	A2	P08581-2
MET	ENST00000436117.3 linkuse as main transcript	c.*1622G>A		3_prime_UTR_variant, NMD_transcript_variant	20/20	1		ENSP00000410980		P08581-3

Frequencies

GnomAD3 genomes

AF:

0.350

AC:

53248

AN:

151968

Hom.:

11164

Cov.:

show subpopulations

Gnomad AFR

AF:

0.101

Gnomad AMI

AF:

0.307

Gnomad AMR

AF:

0.444

Gnomad ASJ

AF:

0.487

Gnomad EAS

AF:

0.470

Gnomad SAS

AF:

0.458

Gnomad FIN

AF:

0.382

Gnomad MID

AF:

0.430

Gnomad NFE

AF:

0.451

Gnomad OTH

AF:

0.391

GnomAD3 exomes

AF:

0.435

AC:

108367

AN:

249310

Hom.:

24773

AF XY:

0.437

AC XY:

59123

AN XY:

135250

show subpopulations

Gnomad AFR exome

AF:

0.0901

Gnomad AMR exome

AF:

0.519

Gnomad ASJ exome

AF:

0.487

Gnomad EAS exome

AF:

0.460

Gnomad SAS exome

AF:

0.460

Gnomad FIN exome

AF:

0.394

Gnomad NFE exome

AF:

0.447

Gnomad OTH exome

AF:

0.457

GnomAD4 exome

AF:

0.444

AC:

649623

AN:

1461836

Hom.:

147170

Cov.:

AF XY:

0.446

AC XY:

323984

AN XY:

727228

show subpopulations

Gnomad4 AFR exome

AF:

0.0877

Gnomad4 AMR exome

AF:

0.511

Gnomad4 ASJ exome

AF:

0.490

Gnomad4 EAS exome

AF:

0.490

Gnomad4 SAS exome

AF:

0.455

Gnomad4 FIN exome

AF:

0.399

Gnomad4 NFE exome

AF:

0.451

Gnomad4 OTH exome

AF:

0.441

GnomAD4 genome

AF:

0.350

AC:

53224

AN:

152086

Hom.:

11151

Cov.:

AF XY:

0.352

AC XY:

26188

AN XY:

74344

show subpopulations

Gnomad4 AFR

AF:

0.101

Gnomad4 AMR

AF:

0.444

Gnomad4 ASJ

AF:

0.487

Gnomad4 EAS

AF:

0.470

Gnomad4 SAS

AF:

0.456

Gnomad4 FIN

AF:

0.382

Gnomad4 NFE

AF:

0.451

Gnomad4 OTH

AF:

0.386

Alfa

AF:

0.423

Hom.:

18065

Bravo

AF:

0.345

Asia WGS

AF:

0.415

AC:

1442

AN:

3478

EpiCase

AF:

0.452

EpiControl

AF:

0.450

ClinVar

Significance: Benign

Submissions summary: Benign:14

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not specified

Benign:7

Benign, no assertion criteria provided	clinical testing	Joint Genome Diagnostic Labs from Nijmegen and Maastricht, Radboudumc and MUMC+	-	- -
Benign, no assertion criteria provided	clinical testing	Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen	-	- -
Benign, criteria provided, single submitter	clinical testing	PreventionGenetics, part of Exact Sciences	-	- -
Benign, no assertion criteria provided	clinical testing	Genome Diagnostics Laboratory, University Medical Center Utrecht	-	- -
Benign, no assertion criteria provided	clinical testing	Clinical Genetics, Academic Medical Center	-	- -
Benign, criteria provided, single submitter	clinical testing	GeneDx	Jan 19, 2016	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, criteria provided, single submitter	clinical testing	Eurofins Ntd Llc (ga)	Jul 30, 2014	- -

Papillary renal cell carcinoma type 1

Benign:2

Benign, criteria provided, single submitter	clinical testing	Illumina Laboratory Services, Illumina	Jan 13, 2018	This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease. -
Benign, criteria provided, single submitter	clinical testing	KCCC/NGS Laboratory, Kuwait Cancer Control Center	Jul 07, 2023	- -

not provided

Benign:2

Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	Women's Health and Genetics/Laboratory Corporation of America, LabCorp	Aug 19, 2016	Variant summary: The c.4071G>A (p.Ala1357=) in MET gene is a synonymous change that involves a non-conserved nucleotide. 5/5 programs in Alamut predict that this variant does not affect normal splicing, however no functional studies supporting this notion were published at the time of evaluation. The variant is present in the control population dataset of ExAC at frequency of 0.4245 (51253/120730chrs tested) including numerous homozygous occurrences. The variant of interest has not, to our knowledge, been reported in affected individuals via publication but is cited as Benign by reputable databases/clinical laboratories. Taking together, based on the prevalence of this variant in general population the variant was classified as Benign. -

Autosomal recessive nonsyndromic hearing loss 97

Benign:1

Benign, criteria provided, single submitter

clinical testing

Genome-Nilou Lab

Sep 05, 2021

- -

Renal cell carcinoma

Benign:1

Benign, criteria provided, single submitter

clinical testing

Labcorp Genetics (formerly Invitae), Labcorp

Feb 01, 2024

- -

Hereditary cancer-predisposing syndrome

Benign:1

Benign, criteria provided, single submitter

clinical testing

Ambry Genetics

Nov 19, 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. -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.72

CADD

Benign

0.19

DANN

Benign

0.72

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

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