5-90558508-A-G

Position:

• chr5-90558508-A-G

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BA1

The ENST00000508842.5(ADGRV1):​c.34+28993A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.483 in 152,012 control chromosomes in the GnomAD database, including 18,419 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.48 (18419 hom., cov: 32)
• Consequence: ADGRV1 ENST00000508842.5 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.311

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]

ACMG classification

Verdict is Benign. Variant got -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.76).
• BP6: Variant 5-90558508-A-G is Benign according to our data. Variant chr5-90558508-A-G is described in ClinVar as [Benign]. Clinvar id is 671524.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.574 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ADGRV1	ENST00000508842.5	c.34+28993A>G		intron_variant	Intron 1 of 3	3		ENSP00000425936.1

Frequencies

GnomAD3 genomes AF: 0.484 AC: 73447 AN: 151894 Hom.: 18403 Cov.: 32

Gnomad AFR AF: 0.354

Gnomad AMI AF: 0.522

Gnomad AMR AF: 0.425

Gnomad ASJ AF: 0.553

Gnomad EAS AF: 0.514

Gnomad SAS AF: 0.591

Gnomad FIN AF: 0.543

Gnomad MID AF: 0.541

Gnomad NFE AF: 0.552

Gnomad OTH AF: 0.481

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.483 AC: 73487 AN: 152012 Hom.: 18419 Cov.: 32 AF XY: 0.486 AC XY: 36075 AN XY: 74290

Gnomad4 AFR AF: 0.355

Gnomad4 AMR AF: 0.424

Gnomad4 ASJ AF: 0.553

Gnomad4 EAS AF: 0.514

Gnomad4 SAS AF: 0.592

Gnomad4 FIN AF: 0.543

Gnomad4 NFE AF: 0.552

Gnomad4 OTH AF: 0.476

Alfa AF: 0.506 Hom.: 2828

Bravo AF: 0.464

Asia WGS AF: 0.512 AC: 1780 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Jun 14, 2018

This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.76
CADD	Benign	5.1
DANN	Benign	0.57

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs154569; hg19: chr5-89854325;