rs2438351

Positions:

• chr5-90762292-G-A
• chr5-90762292-G-C
• chr5-90762292-G-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_032119.4(ADGRV1):​c.12121-1013G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.641 in 151,904 control chromosomes in the GnomAD database, including 31,988 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.64 (31988 hom., cov: 32)
• Consequence: ADGRV1 NM_032119.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.00600

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 -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.803 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ADGRV1	NM_032119.4	c.12121-1013G>A		intron_variant		ENST00000405460.9	NP_115495.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ADGRV1	ENST00000405460.9	c.12121-1013G>A		intron_variant		1	NM_032119.4	ENSP00000384582	P1
ADGRV1	ENST00000425867.3	c.1075-1013G>A		intron_variant		5		ENSP00000392618
ADGRV1	ENST00000639431.1	c.265+86083G>A		intron_variant, NMD_transcript_variant		5		ENSP00000491057
ADGRV1	ENST00000640464.1	n.2540-1013G>A		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.641 AC: 97306 AN: 151786 Hom.: 31950 Cov.: 32

Gnomad AFR AF: 0.763

Gnomad AMI AF: 0.546

Gnomad AMR AF: 0.715

Gnomad ASJ AF: 0.524

Gnomad EAS AF: 0.824

Gnomad SAS AF: 0.685

Gnomad FIN AF: 0.576

Gnomad MID AF: 0.611

Gnomad NFE AF: 0.551

Gnomad OTH AF: 0.644

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

GnomAD4 genome AF: 0.641 AC: 97400 AN: 151904 Hom.: 31988 Cov.: 32 AF XY: 0.646 AC XY: 47927 AN XY: 74230

Gnomad4 AFR AF: 0.763

Gnomad4 AMR AF: 0.716

Gnomad4 ASJ AF: 0.524

Gnomad4 EAS AF: 0.823

Gnomad4 SAS AF: 0.683

Gnomad4 FIN AF: 0.576

Gnomad4 NFE AF: 0.551

Gnomad4 OTH AF: 0.648

Alfa AF: 0.573 Hom.: 21372

Bravo AF: 0.656

Asia WGS AF: 0.775 AC: 2693 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	6.6
DANN	Benign	0.39

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

LitVar

Other links and lift over

dbSNP: rs2438351; hg19: chr5-90058109;