rs10060641

Variant names:

• chr5-90917433-T-C
• rs10060641
• NM_032119.4:c.17857-47982T>C

Variant summary

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

The NM_032119.4(ADGRV1):​c.17857-47982T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.281 in 150,908 control chromosomes in the GnomAD database, including 6,467 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 0.28 (6467 hom., cov: 31)
• Consequence: ADGRV1 NM_032119.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0580

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=-0.84).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.342 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ADGRV1	NM_032119.4	c.17857-47982T>C		intron_variant	Intron 83 of 89	ENST00000405460.9	NP_115495.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ADGRV1	ENST00000405460.9	c.17857-47982T>C		intron_variant	Intron 83 of 89	1	NM_032119.4	ENSP00000384582.2

Frequencies

GnomAD3 genomes AF: 0.281 AC: 42362 AN: 150792 Hom.: 6464 Cov.: 31

Gnomad AFR AF: 0.181

Gnomad AMI AF: 0.354

Gnomad AMR AF: 0.262

Gnomad ASJ AF: 0.283

Gnomad EAS AF: 0.182

Gnomad SAS AF: 0.227

Gnomad FIN AF: 0.332

Gnomad MID AF: 0.301

Gnomad NFE AF: 0.346

Gnomad OTH AF: 0.300

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

GnomAD4 genome AF: 0.281 AC: 42391 AN: 150908 Hom.: 6467 Cov.: 31 AF XY: 0.280 AC XY: 20626 AN XY: 73792

Gnomad4 AFR AF: 0.181

Gnomad4 AMR AF: 0.262

Gnomad4 ASJ AF: 0.283

Gnomad4 EAS AF: 0.183

Gnomad4 SAS AF: 0.227

Gnomad4 FIN AF: 0.332

Gnomad4 NFE AF: 0.346

Gnomad4 OTH AF: 0.304

Alfa AF: 0.334 Hom.: 17350

Bravo AF: 0.271

Asia WGS AF: 0.223 AC: 774 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	4.5
DANN	Benign	0.78

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: rs10060641; hg19: chr5-90213250;