chr5-90558666-G-A

Variant names:

• chr5-90558666-G-A
• rs114738440
• ENST00000508842.5:c.34+29151G>A

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+29151G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00611 in 671,900 control chromosomes in the GnomAD database, including 118 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.019 (86 hom., cov: 32)
  • Exomes 𝑓: 0.0025 (32 hom.)
• Consequence: ADGRV1 ENST00000508842.5 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.248

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=-0.48).
• BP6: Variant 5-90558666-G-A is Benign according to our data. Variant chr5-90558666-G-A is described in ClinVar as [Benign]. Clinvar id is 1243078.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0626 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+29151G>A		intron_variant	Intron 1 of 3	3		ENSP00000425936.1
ADGRV1	ENST00000638316.1	n.-20G>A		upstream_gene_variant		5

Frequencies

GnomAD3 genomes AF: 0.0186 AC: 2823 AN: 152080 Hom.: 87 Cov.: 32

Gnomad AFR AF: 0.0647

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00654

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.000207

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00316

Gnomad NFE AF: 0.000250

Gnomad OTH AF: 0.0119

GnomAD4 exome AF: 0.00245 AC: 1275 AN: 519702 Hom.: 32 Cov.: 4 AF XY: 0.00199 AC XY: 556 AN XY: 279512

Gnomad4 AFR exome AF: 0.0645

Gnomad4 AMR exome AF: 0.00366

Gnomad4 ASJ exome AF: 0.0000542

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.000119

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.000153

Gnomad4 OTH exome AF: 0.00467

GnomAD4 genome AF: 0.0186 AC: 2828 AN: 152198 Hom.: 86 Cov.: 32 AF XY: 0.0173 AC XY: 1290 AN XY: 74410

Gnomad4 AFR AF: 0.0646

Gnomad4 AMR AF: 0.00653

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.000208

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.000250

Gnomad4 OTH AF: 0.0118

Alfa AF: 0.00319 Hom.: 2

Bravo AF: 0.0214

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

Aug 13, 2018

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.48
CADD	Benign	5.8
DANN	Benign	0.94

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs114738440; hg19: chr5-89854483;