chr5-90728918-G-A

Variant names:

Variant summary

Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP6_Very_StrongBA1

The NM_032119.4(ADGRV1):c.10411G>A(p.Glu3471Lys) variant causes a missense change. The variant allele was found at a frequency of 0.711 in 1,605,000 control chromosomes in the GnomAD database, including 409,901 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.77 ( 45573 hom., cov: 32)

Exomes 𝑓: 0.71 ( 364328 hom. )

Consequence

ADGRV1
NM_032119.4 missense

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:11

Conservation

PhyloP100: 4.39

Variant links:

Genes affected

ADGRV1 (HGNC:17416): (adhesion G protein-coupled receptor V1) This gene encodes a member of the G-protein coupled receptor superfamily. The encoded protein contains a 7-transmembrane receptor domain, binds calcium and is expressed in the central nervous system. Mutations in this gene are associated with Usher syndrome 2 and familial febrile seizures. Several alternatively spliced transcripts have been described. [provided by RefSeq, Jul 2008]

ADGRV1 links:

LOC105379077 (HGNC:):

LOC105379077 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -16 ACMG points.

BP6

Variant 5-90728918-G-A is Benign according to our data. Variant chr5-90728918-G-A is described in ClinVar as [Benign]. Clinvar id is 46248.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr5-90728918-G-A is described in Lovd as [Benign].

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.895 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ADGRV1	NM_032119.4 link	c.10411G>A	p.Glu3471Lys	missense_variant	Exon 49 of 90	ENST00000405460.9	NP_115495.3	Q8WXG9-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ADGRV1	ENST00000405460.9 link	c.10411G>A	p.Glu3471Lys	missense_variant	Exon 49 of 90	1	NM_032119.4	ENSP00000384582.2		Q8WXG9-1

Frequencies

GnomAD3 genomes

AF:

0.768

AC:

116702

AN:

152048

Hom.:

45497

Cov.:

show subpopulations

Gnomad AFR

AF:

0.902

Gnomad AMI

AF:

0.663

Gnomad AMR

AF:

0.804

Gnomad ASJ

AF:

0.727

Gnomad EAS

AF:

0.801

Gnomad SAS

AF:

0.816

Gnomad FIN

AF:

0.733

Gnomad MID

AF:

0.715

Gnomad NFE

AF:

0.680

Gnomad OTH

AF:

0.763

GnomAD3 exomes

AF:

0.750

AC:

185376

AN:

247166

Hom.:

70243

AF XY:

0.745

AC XY:

99855

AN XY:

134072

show subpopulations

Gnomad AFR exome

AF:

0.909

Gnomad AMR exome

AF:

0.852

Gnomad ASJ exome

AF:

0.720

Gnomad EAS exome

AF:

0.785

Gnomad SAS exome

AF:

0.815

Gnomad FIN exome

AF:

0.728

Gnomad NFE exome

AF:

0.681

Gnomad OTH exome

AF:

0.728

GnomAD4 exome

AF:

0.705

AC:

1024823

AN:

1452834

Hom.:

364328

Cov.:

AF XY:

0.707

AC XY:

511177

AN XY:

722816

show subpopulations

Gnomad4 AFR exome

AF:

0.908

Gnomad4 AMR exome

AF:

0.846

Gnomad4 ASJ exome

AF:

0.722

Gnomad4 EAS exome

AF:

0.804

Gnomad4 SAS exome

AF:

0.814

Gnomad4 FIN exome

AF:

0.727

Gnomad4 NFE exome

AF:

0.679

Gnomad4 OTH exome

AF:

0.728

GnomAD4 genome

AF:

0.768

AC:

116841

AN:

152166

Hom.:

45573

Cov.:

AF XY:

0.774

AC XY:

57609

AN XY:

74398

show subpopulations

Gnomad4 AFR

AF:

0.903

Gnomad4 AMR

AF:

0.805

Gnomad4 ASJ

AF:

0.727

Gnomad4 EAS

AF:

0.802

Gnomad4 SAS

AF:

0.815

Gnomad4 FIN

AF:

0.733

Gnomad4 NFE

AF:

0.681

Gnomad4 OTH

AF:

0.766

Alfa

AF:

0.705

Hom.:

88465

Bravo

AF:

0.779

TwinsUK

AF:

0.676

AC:

2508

ALSPAC

AF:

0.693

AC:

2669

ESP6500AA

AF:

0.904

AC:

3307

ESP6500EA

AF:

0.686

AC:

5602

ExAC

AF:

0.748

AC:

90266

Asia WGS

AF:

0.847

AC:

2943

AN:

3478

EpiCase

AF:

0.694

EpiControl

AF:

0.691

ClinVar

Significance: Benign

Submissions summary: Benign:11

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not specified

Benign:6

Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen

Significance: Benign

Review Status: no assertion criteria provided

Collection Method: clinical testing

- -

Mar 23, 2010

Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Jan 21, 2015

Eurofins Ntd Llc (ga)

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

PreventionGenetics, part of Exact Sciences

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Genetic Services Laboratory, University of Chicago

Significance: Likely benign

Review Status: no assertion criteria provided

Collection Method: clinical testing

- -

Joint Genome Diagnostic Labs from Nijmegen and Maastricht, Radboudumc and MUMC+

Significance: Benign

Review Status: no assertion criteria provided

Collection Method: clinical testing

- -

not provided

Benign:3

Feb 03, 2025

Labcorp Genetics (formerly Invitae), Labcorp

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Mar 03, 2015

GeneDx

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Apr 20, 2017

Athena Diagnostics

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Usher syndrome type 2C

Benign:2

Aug 10, 2021

Genome-Nilou Lab

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Jan 13, 2018

Illumina Laboratory Services, Illumina

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

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. -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.044

BayesDel_addAF

Benign

-0.57

BayesDel_noAF

Benign

-0.45

CADD

Benign

DANN

Benign

0.31

DEOGEN2

Benign

0.074

T;T

Eigen

Benign

-0.88

Eigen_PC

Benign

-0.58

FATHMM_MKL

Benign

0.024

LIST_S2

Benign

0.37

.;T

MetaRNN

Benign

6.6e-7

T;T

MetaSVM

Benign

-0.96

PrimateAI

Benign

0.45

PROVEAN

Benign

0.86

.;N

REVEL

Benign

0.17

Sift

Benign

1.0

.;T

Sift4G

Benign

1.0

.;T

Polyphen

0.0

B;B

Vest4

0.084

MPC

0.052

ClinPred

0.0083

GERP RS

5.6

Varity_R

0.055

gMVP

0.34

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.30

Details are displayed if max score is > 0.2

DS_DL_spliceai

0.30

Position offset: 15

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