Variant chr6-159907710-A-G details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP6_ModerateBS2

The NM_002377.4(MAS1):c.755A>G(p.Tyr252Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00234 in 1,613,268 control chromosomes in the GnomAD database, including 7 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.0020 ( 1 hom., cov: 30)

Exomes 𝑓: 0.0024 ( 6 hom. )

Consequence

MAS1
NM_002377.4 missense

Scores

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: 2.07

Variant links:

Genes affected

MAS1 (HGNC:6899): (MAS1 proto-oncogene, G protein-coupled receptor) This gene encodes a class I seven-transmembrane G-protein-coupled receptor. The encoded protein is a receptor for angiotensin-(1-7) and preferentially couples to the Gq protein, activating the phospholipase C signaling pathway. The encoded protein may play a role in multiple processes including hypotension, smooth muscle relaxation and cardioprotection by mediating the effects of angiotensin-(1-7). [provided by RefSeq, May 2012]

MAS1 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -6 ACMG points.

BP6

Variant 6-159907710-A-G is Benign according to our data. Variant chr6-159907710-A-G is described in ClinVar as [Likely_benign]. Clinvar id is 719390.Status of the report is criteria_provided_single_submitter, 1 stars.

BS2

High Homozygotes in GnomAdExome4 at 6 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE
MAS1	NM_002377.4 linkuse as main transcript	c.755A>G	p.Tyr252Cys	missense_variant	3/3	ENST00000674077.2
MAS1	NM_001366704.2 linkuse as main transcript	c.755A>G	p.Tyr252Cys	missense_variant	2/2
MAS1	XM_047418776.1 linkuse as main transcript	c.755A>G	p.Tyr252Cys	missense_variant	4/4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MAS1	ENST00000674077.2 linkuse as main transcript	c.755A>G	p.Tyr252Cys	missense_variant	3/3		NM_002377.4	P1
MAS1	ENST00000252660.5 linkuse as main transcript	c.755A>G	p.Tyr252Cys	missense_variant	1/1			P1

Frequencies

GnomAD3 genomes

AF:

0.00201

AC:

305

AN:

151432

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.000485

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00290

Gnomad ASJ

AF:

0.00260

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00127

Gnomad FIN

AF:

0.00114

Gnomad MID

AF:

0.00633

Gnomad NFE

AF:

0.00304

Gnomad OTH

AF:

0.00290

GnomAD3 exomes

AF:

0.00242

AC:

608

AN:

251392

Hom.:

AF XY:

0.00244

AC XY:

332

AN XY:

135862

show subpopulations

Gnomad AFR exome

AF:

0.000615

Gnomad AMR exome

AF:

0.00168

Gnomad ASJ exome

AF:

0.00129

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.000588

Gnomad FIN exome

AF:

0.00129

Gnomad NFE exome

AF:

0.00405

Gnomad OTH exome

AF:

0.00343

GnomAD4 exome

AF:

0.00238

AC:

3472

AN:

1461718

Hom.:

Cov.:

AF XY:

0.00239

AC XY:

1739

AN XY:

727166

show subpopulations

Gnomad4 AFR exome

AF:

0.000568

Gnomad4 AMR exome

AF:

0.00212

Gnomad4 ASJ exome

AF:

0.00157

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.000812

Gnomad4 FIN exome

AF:

0.00172

Gnomad4 NFE exome

AF:

0.00269

Gnomad4 OTH exome

AF:

0.00245

GnomAD4 genome

AF:

0.00200

AC:

303

AN:

151550

Hom.:

Cov.:

AF XY:

0.00200

AC XY:

148

AN XY:

74026

show subpopulations

Gnomad4 AFR

AF:

0.000484

Gnomad4 AMR

AF:

0.00290

Gnomad4 ASJ

AF:

0.00260

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00127

Gnomad4 FIN

AF:

0.00114

Gnomad4 NFE

AF:

0.00301

Gnomad4 OTH

AF:

0.00287

Alfa

AF:

0.00284

Hom.:

Bravo

AF:

0.00209

TwinsUK

AF:

0.00216

AC:

ALSPAC

AF:

0.00156

AC:

ESP6500AA

AF:

0.00

AC:

ESP6500EA

AF:

0.00326

AC:

ExAC

AF:

0.00299

AC:

363

Asia WGS

AF:

0.000289

AC:

AN:

3478

EpiCase

AF:

0.00387

EpiControl

AF:

0.00267

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Likely benign, criteria provided, single submitter

clinical testing

Invitae

Jul 10, 2018

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.32

BayesDel_addAF

Benign

-0.34

BayesDel_noAF

Benign

-0.26

CADD

Pathogenic

DANN

Uncertain

1.0

DEOGEN2

Benign

0.38

Eigen

Uncertain

0.27

Eigen_PC

Benign

0.17

FATHMM_MKL

Uncertain

0.77

LIST_S2

Uncertain

0.93

M_CAP

Benign

0.021

MetaRNN

Benign

0.026

MetaSVM

Benign

-0.96

MutationAssessor

Uncertain

2.1

MutationTaster

Benign

0.83

PrimateAI

Uncertain

0.55

PROVEAN

Uncertain

-2.9

REVEL

Benign

0.25

Sift

Uncertain

0.016

Sift4G

Uncertain

0.048

Polyphen

1.0

Vest4

0.66

MVP

0.81

MPC

0.54

ClinPred

0.022

GERP RS

4.0

Varity_R

0.37

gMVP

0.51

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.76

Details are displayed if max score is > 0.2

DS_DG_spliceai

0.76

Position offset: -1

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