rs377585302

Variant names:

Variant summary

Our verdict is Benign. The variant received -16 ACMG points: 0P and 16B. BP6_Very_StrongBA1

The NM_032119.4(ADGRV1):c.8730+10_8730+11insC variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00583 in 701,856 control chromosomes in the GnomAD database, including 82 homozygotes. Variant has been reported in ClinVar as Likely benign (★★).

Frequency

Genomes: 𝑓 0.071 ( 33 hom., cov: 31)

Exomes 𝑓: 0.0044 ( 49 hom. )

Consequence

ADGRV1
NM_032119.4 intron

Scores

Not classified

Clinical Significance

Benign/Likely benign criteria provided, multiple submitters, no conflicts B:6

Conservation

PhyloP100: 1.54

Publications

3 publications found

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 Gene-Disease associations (from GenCC):

Usher syndrome type 2
Inheritance: AR Classification: DEFINITIVE, SUPPORTIVE Submitted by: ClinGen, Orphanet
Usher syndrome type 2C
Inheritance: AR Classification: STRONG Submitted by: G2P, PanelApp Australia, Labcorp Genetics (formerly Invitae)
febrile seizures, familial, 4
Inheritance: AD Classification: LIMITED Submitted by: Ambry Genetics
nonsyndromic genetic hearing loss
Inheritance: AR Classification: NO_KNOWN Submitted by: ClinGen

ADGRV1 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -16 ACMG points.

BP6

Variant 5-90706404-T-TC is Benign according to our data. Variant chr5-90706404-T-TC is described in ClinVar as [Likely_benign]. Clinvar id is 46397.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.337 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ADGRV1	NM_032119.4 link	c.8730+10_8730+11insC		intron_variant	Intron 38 of 89	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.8730+10_8730+11insC		intron_variant	Intron 38 of 89	1	NM_032119.4	ENSP00000384582.2		Q8WXG9-1

Frequencies

GnomAD3 genomes

AF:

0.0703

AC:

1047

AN:

14892

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0632

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.355

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.211

Gnomad SAS

AF:

0.0139

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.000690

Gnomad OTH

AF:

0.157

GnomAD2 exomes

AF:

0.0669

AC:

1799

AN:

26884

AF XY:

0.0563

show subpopulations

Gnomad AFR exome

AF:

0.0200

Gnomad AMR exome

AF:

0.327

Gnomad ASJ exome

AF:

0.00

Gnomad EAS exome

AF:

0.120

Gnomad FIN exome

AF:

0.00

Gnomad NFE exome

AF:

0.000612

Gnomad OTH exome

AF:

0.0531

GnomAD4 exome

AF:

0.00442

AC:

3037

AN:

686940

Hom.:

Cov.:

AF XY:

0.00406

AC XY:

1374

AN XY:

338096

show subpopulations

African (AFR)

AF:

0.00171

AC:

AN:

18160

American (AMR)

AF:

0.130

AC:

2318

AN:

17784

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

11436

East Asian (EAS)

AF:

0.0184

AC:

423

AN:

22964

South Asian (SAS)

AF:

0.00135

AC:

AN:

36286

European-Finnish (FIN)

AF:

0.00

AC:

AN:

28508

Middle Eastern (MID)

AF:

0.00

AC:

AN:

3570

European-Non Finnish (NFE)

AF:

0.0000655

AC:

AN:

518906

Other (OTH)

AF:

0.00621

AC:

182

AN:

29326

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.450

Heterozygous variant carriers

114

228

342

456

570

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

AF:

0.0709

AC:

1057

AN:

14916

Hom.:

Cov.:

AF XY:

0.0813

AC XY:

592

AN XY:

7282

show subpopulations

African (AFR)

AF:

0.0631

AC:

AN:

1362

American (AMR)

AF:

0.357

AC:

850

AN:

2380

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

368

East Asian (EAS)

AF:

0.210

AC:

AN:

396

South Asian (SAS)

AF:

0.0136

AC:

AN:

368

European-Finnish (FIN)

AF:

0.00

AC:

AN:

1086

Middle Eastern (MID)

AF:

0.00

AC:

AN:

European-Non Finnish (NFE)

AF:

0.000690

AC:

AN:

8700

Other (OTH)

AF:

0.157

AC:

AN:

172

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

140

187

234

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Alfa

AF:

0.00556

Hom.:

ClinVar

Significance: Benign/Likely benign

Submissions summary: Benign:6

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:3

May 04, 2018

GeneDx

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

- -

Oct 02, 2018

Athena Diagnostics

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

- -

Feb 03, 2025

Labcorp Genetics (formerly Invitae), Labcorp

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

- -

not specified

Benign:2

Nov 07, 2014

Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

c.8730+10_8730+11insC in intron 38 of GPR98: This variant is not expected to hav e clinical significance because it has been identified in 4.2% (15/358) of Latin American (Puerto Rican, Mexican-American, Columbian) chromosomes and 2.4% (14/5 72) of East Asian (Chinese and Japanese) chromosomes by the 1000 Genomes Project (dbSNP rs377585302). -

Dec 19, 2014

Eurofins Ntd Llc (ga)

Significance:Likely benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

- -

Febrile seizures, familial, 4;C2931213:Usher syndrome type 2C

Benign:1

Mar 28, 2022

Fulgent Genetics, Fulgent Genetics

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

PhyloP100

1.5

Mutation Taster

=23/77

disease causing (long InDel)

(source)

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

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rs377585302

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

Other links and lift over