Variant 19-53258520-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2

The NM_173856.2(VN1R2):c.145C>T(p.Arg49Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00499 in 1,467,742 control chromosomes in the GnomAD database, including 32 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.0042 ( 4 hom., cov: 32)

Exomes 𝑓: 0.0051 ( 28 hom. )

Consequence

VN1R2
NM_173856.2 missense

Scores

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.254

Variant links:

Genes affected

VN1R2 (HGNC:19872): (vomeronasal 1 receptor 2) Predicted to enable pheromone receptor activity. Predicted to be involved in G protein-coupled receptor signaling pathway and response to pheromone. Predicted to be located in plasma membrane. Predicted to be integral component of membrane. [provided by Alliance of Genome Resources, Apr 2022]

VN1R2 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -10 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.004188299).

BP6

Variant 19-53258520-C-T is Benign according to our data. Variant chr19-53258520-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 2650409.Status of the report is criteria_provided_single_submitter, 1 stars.

BS2

High Homozygotes in GnomAd4 at 4 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
VN1R2	NM_173856.2 linkuse as main transcript	c.145C>T	p.Arg49Cys	missense_variant	1/1	ENST00000341702.3	NP_776255.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
VN1R2	ENST00000341702.3 linkuse as main transcript	c.145C>T	p.Arg49Cys	missense_variant	1/1		NM_173856.2	ENSP00000351244	P1

Frequencies

GnomAD3 genomes

AF:

0.00424

AC:

646

AN:

152182

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00118

Gnomad AMI

AF:

0.00110

Gnomad AMR

AF:

0.00288

Gnomad ASJ

AF:

0.0156

Gnomad EAS

AF:

0.000193

Gnomad SAS

AF:

0.000414

Gnomad FIN

AF:

0.00122

Gnomad MID

AF:

0.00633

Gnomad NFE

AF:

0.00697

Gnomad OTH

AF:

0.00287

GnomAD3 exomes

AF:

0.00370

AC:

576

AN:

155586

Hom.:

AF XY:

0.00372

AC XY:

306

AN XY:

82228

show subpopulations

Gnomad AFR exome

AF:

0.00133

Gnomad AMR exome

AF:

0.00210

Gnomad ASJ exome

AF:

0.00859

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.000567

Gnomad FIN exome

AF:

0.00286

Gnomad NFE exome

AF:

0.00595

Gnomad OTH exome

AF:

0.00596

GnomAD4 exome

AF:

0.00508

AC:

6682

AN:

1315442

Hom.:

Cov.:

AF XY:

0.00509

AC XY:

3328

AN XY:

653208

show subpopulations

Gnomad4 AFR exome

AF:

0.00113

Gnomad4 AMR exome

AF:

0.00290

Gnomad4 ASJ exome

AF:

0.0109

Gnomad4 EAS exome

AF:

0.0000566

Gnomad4 SAS exome

AF:

0.000516

Gnomad4 FIN exome

AF:

0.00189

Gnomad4 NFE exome

AF:

0.00586

Gnomad4 OTH exome

AF:

0.00465

GnomAD4 genome

AF:

0.00424

AC:

645

AN:

152300

Hom.:

Cov.:

AF XY:

0.00408

AC XY:

304

AN XY:

74476

show subpopulations

Gnomad4 AFR

AF:

0.00118

Gnomad4 AMR

AF:

0.00288

Gnomad4 ASJ

AF:

0.0156

Gnomad4 EAS

AF:

0.000193

Gnomad4 SAS

AF:

0.000415

Gnomad4 FIN

AF:

0.00122

Gnomad4 NFE

AF:

0.00695

Gnomad4 OTH

AF:

0.00284

Alfa

AF:

0.00619

Hom.:

Bravo

AF:

0.00423

TwinsUK

AF:

0.00728

AC:

ALSPAC

AF:

0.00441

AC:

ESP6500AA

AF:

0.000249

AC:

ESP6500EA

AF:

0.00542

AC:

ExAC

AF:

0.00167

AC:

129

Asia WGS

AF:

0.00144

AC:

AN:

3478

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

CeGaT Center for Human Genetics Tuebingen

Dec 01, 2022

VN1R2: BS2 -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.14

BayesDel_addAF

Benign

-0.59

BayesDel_noAF

Benign

-0.62

CADD

Benign

DANN

Benign

0.49

DEOGEN2

Benign

0.00076

Eigen

Benign

-0.74

Eigen_PC

Benign

-0.98

FATHMM_MKL

Benign

0.0021

LIST_S2

Benign

0.40

MetaRNN

Benign

0.0042

MetaSVM

Benign

-1.0

MutationAssessor

Benign

0.0

MutationTaster

Benign

1.0

PrimateAI

Uncertain

0.51

PROVEAN

Benign

-0.040

REVEL

Benign

0.079

Sift

Pathogenic

0.0

Polyphen

0.98

Vest4

0.24

MVP

0.13

MPC

0.17

ClinPred

0.027

GERP RS

0.046

Varity_R

0.13

gMVP

0.38

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