Variant 12-63150429-A-G details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6BP7BA1

The NM_000706.5(AVPR1A):c.408T>C(p.Phe136=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.588 in 1,612,908 control chromosomes in the GnomAD database, including 282,406 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (no stars).

Frequency

Genomes: 𝑓 0.65 ( 33256 hom., cov: 34)

Exomes 𝑓: 0.58 ( 249150 hom. )

Consequence

AVPR1A
NM_000706.5 synonymous

Scores

Clinical Significance

Benign no assertion criteria provided B:1

Conservation

PhyloP100: 2.93

Variant links:

Genes affected

AVPR1A (HGNC:895): (arginine vasopressin receptor 1A) The protein encoded by this gene acts as receptor for arginine vasopressin. This receptor belongs to the subfamily of G-protein coupled receptors which includes AVPR1B, V2R and OXT receptors. Its activity is mediated by G proteins which stimulate a phosphatidylinositol-calcium second messenger system. The receptor mediates cell contraction and proliferation, platelet aggregation, release of coagulation factor and glycogenolysis. [provided by RefSeq, Jul 2008]

AVPR1A links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -14 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.57).

BP6

Variant 12-63150429-A-G is Benign according to our data. Variant chr12-63150429-A-G is described in ClinVar as [Benign]. Clinvar id is 3060712.Status of the report is no_assertion_criteria_provided, 0 stars. Variant chr12-63150429-A-G is described in Lovd as [Benign].

BP7

Synonymous conserved (PhyloP=2.93 with no splicing effect.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.823 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
AVPR1A	NM_000706.5 linkuse as main transcript	c.408T>C	p.Phe136=	synonymous_variant	1/2	ENST00000299178.4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
AVPR1A	ENST00000299178.4 linkuse as main transcript	c.408T>C	p.Phe136=	synonymous_variant	1/2	1	NM_000706.5	P1

Frequencies

GnomAD3 genomes

AF:

0.651

AC:

98958

AN:

152054

Hom.:

33210

Cov.:

show subpopulations

Gnomad AFR

AF:

0.831

Gnomad AMI

AF:

0.556

Gnomad AMR

AF:

0.631

Gnomad ASJ

AF:

0.685

Gnomad EAS

AF:

0.450

Gnomad SAS

AF:

0.690

Gnomad FIN

AF:

0.583

Gnomad MID

AF:

0.699

Gnomad NFE

AF:

0.567

Gnomad OTH

AF:

0.668

GnomAD3 exomes

AF:

0.604

AC:

149460

AN:

247436

Hom.:

46034

AF XY:

0.603

AC XY:

81063

AN XY:

134352

show subpopulations

Gnomad AFR exome

AF:

0.834

Gnomad AMR exome

AF:

0.605

Gnomad ASJ exome

AF:

0.691

Gnomad EAS exome

AF:

0.449

Gnomad SAS exome

AF:

0.689

Gnomad FIN exome

AF:

0.575

Gnomad NFE exome

AF:

0.570

Gnomad OTH exome

AF:

0.612

GnomAD4 exome

AF:

0.581

AC:

848579

AN:

1460734

Hom.:

249150

Cov.:

AF XY:

0.583

AC XY:

423812

AN XY:

726642

show subpopulations

Gnomad4 AFR exome

AF:

0.837

Gnomad4 AMR exome

AF:

0.610

Gnomad4 ASJ exome

AF:

0.686

Gnomad4 EAS exome

AF:

0.496

Gnomad4 SAS exome

AF:

0.689

Gnomad4 FIN exome

AF:

0.582

Gnomad4 NFE exome

AF:

0.562

Gnomad4 OTH exome

AF:

0.609

GnomAD4 genome

AF:

0.651

AC:

99060

AN:

152174

Hom.:

33256

Cov.:

AF XY:

0.651

AC XY:

48460

AN XY:

74384

show subpopulations

Gnomad4 AFR

AF:

0.831

Gnomad4 AMR

AF:

0.631

Gnomad4 ASJ

AF:

0.685

Gnomad4 EAS

AF:

0.451

Gnomad4 SAS

AF:

0.691

Gnomad4 FIN

AF:

0.583

Gnomad4 NFE

AF:

0.567

Gnomad4 OTH

AF:

0.663

Alfa

AF:

0.580

Hom.:

23248

Bravo

AF:

0.657

Asia WGS

AF:

0.593

AC:

2062

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: no assertion criteria provided

LINK: link

Submissions by phenotype

AVPR1A-related disorder

Benign:1

Benign, no assertion criteria provided

clinical testing

PreventionGenetics, part of Exact Sciences

Feb 22, 2022

This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.57

CADD

Benign

8.7

DANN

Benign

0.91

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