Variant chr5-90558750-G-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2

The ENST00000508842.5(ADGRV1):c.34+29235G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00445 in 783,846 control chromosomes in the GnomAD database, including 44 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).

Frequency

Genomes: 𝑓 0.0042 ( 5 hom., cov: 32)

Exomes 𝑓: 0.0045 ( 39 hom. )

Consequence

ADGRV1
ENST00000508842.5 intron

Scores

Clinical Significance

Likely benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: -0.605

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:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.81).

BP6

Variant 5-90558750-G-A is Benign according to our data. Variant chr5-90558750-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 1210776.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BS1

Variant frequency is greater than expected in population sas. gnomad4 allele frequency = 0.00422 (642/152188) while in subpopulation SAS AF= 0.0147 (71/4824). AF 95% confidence interval is 0.012. There are 5 homozygotes in gnomad4. There are 323 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.

BS2

High Homozygotes in GnomAd4 at 5 AR,Digenic gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ADGRV1	NM_032119.4 linkuse as main transcript			upstream_gene_variant		ENST00000405460.9	NP_115495.3

Ensembl

Gene	Transcript	HGVSc	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ADGRV1	ENST00000508842.5 linkuse as main transcript	c.34+29235G>A	intron_variant		3		ENSP00000425936
ADGRV1	ENST00000638316.1 linkuse as main transcript	n.65G>A	non_coding_transcript_exon_variant	1/6	5
ADGRV1	ENST00000405460.9 linkuse as main transcript		upstream_gene_variant		1	NM_032119.4	ENSP00000384582	P1	Q8WXG9-1
ADGRV1	ENST00000640109.1 linkuse as main transcript		upstream_gene_variant		5

Frequencies

GnomAD3 genomes

AF:

0.00424

AC:

645

AN:

152070

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00722

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00380

Gnomad ASJ

AF:

0.0144

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.0149

Gnomad FIN

AF:

0.0000942

Gnomad MID

AF:

0.0253

Gnomad NFE

AF:

0.00201

Gnomad OTH

AF:

0.00957

GnomAD3 exomes

AF:

0.00602

AC:

866

AN:

143888

Hom.:

AF XY:

0.00695

AC XY:

537

AN XY:

77216

show subpopulations

Gnomad AFR exome

AF:

0.00710

Gnomad AMR exome

AF:

0.00428

Gnomad ASJ exome

AF:

0.0133

Gnomad EAS exome

AF:

0.000185

Gnomad SAS exome

AF:

0.0179

Gnomad FIN exome

AF:

0.000127

Gnomad NFE exome

AF:

0.00250

Gnomad OTH exome

AF:

0.0102

GnomAD4 exome

AF:

0.00451

AC:

2846

AN:

631658

Hom.:

Cov.:

AF XY:

0.00517

AC XY:

1745

AN XY:

337348

show subpopulations

Gnomad4 AFR exome

AF:

0.00684

Gnomad4 AMR exome

AF:

0.00429

Gnomad4 ASJ exome

AF:

0.0135

Gnomad4 EAS exome

AF:

0.0000928

Gnomad4 SAS exome

AF:

0.0167

Gnomad4 FIN exome

AF:

0.000127

Gnomad4 NFE exome

AF:

0.00215

Gnomad4 OTH exome

AF:

0.00688

GnomAD4 genome

AF:

0.00422

AC:

642

AN:

152188

Hom.:

Cov.:

AF XY:

0.00434

AC XY:

323

AN XY:

74424

show subpopulations

Gnomad4 AFR

AF:

0.00717

Gnomad4 AMR

AF:

0.00379

Gnomad4 ASJ

AF:

0.0144

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.0147

Gnomad4 FIN

AF:

0.0000942

Gnomad4 NFE

AF:

0.00202

Gnomad4 OTH

AF:

0.00994

Alfa

AF:

0.00360

Hom.:

Bravo

AF:

0.00418

Asia WGS

AF:

0.00664

AC:

AN:

3478

ClinVar

Significance: Likely benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Likely benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Likely benign, criteria provided, single submitter	clinical testing	GeneDx	Dec 31, 2018	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.81

CADD

Benign

4.8

DANN

Benign

0.65

Splicing

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