rs3098356

Variant names:

• chr5-90872194-C-A
• rs3098356
• NM_032119.4:c.17856+8337C>A

Your query was ambiguous. Multiple possible variants found:

• chr5-90872194-C-A
• chr5-90872194-C-G
• chr5-90872194-C-T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_032119.4(ADGRV1):​c.17856+8337C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.589 in 151,972 control chromosomes in the GnomAD database, including 26,847 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 0.59 (26847 hom., cov: 31)
• Consequence: ADGRV1 NM_032119.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.95
• Publications: 5 publications found

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 Gene-Disease associations (from GenCC):

• Usher syndrome type 2

  Inheritance: AR Classification: DEFINITIVE, SUPPORTIVE Submitted by: ClinGen, Orphanet
• Usher syndrome type 2C

  Inheritance: AR Classification: STRONG Submitted by: G2P, Labcorp Genetics (formerly Invitae)
• febrile seizures, familial, 4

  Inheritance: AD Classification: LIMITED Submitted by: Ambry Genetics
• nonsyndromic genetic hearing loss

  Inheritance: AR Classification: NO_KNOWN Submitted by: ClinGen

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.807 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_032119.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ADGRV1	NM_032119.4	MANE Select	c.17856+8337C>A		intron	N/A	NP_115495.3	Q8WXG9-1
	ADGRV1	NR_003149.2		n.17872+8337C>A		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ADGRV1	ENST00000405460.9	TSL:1 MANE Select	c.17856+8337C>A		intron	N/A	ENSP00000384582.2	Q8WXG9-1
	ADGRV1	ENST00000638510.1	TSL:1	n.5123+8337C>A		intron	N/A
	ADGRV1	ENST00000425867.3	TSL:5	c.6810+8337C>A		intron	N/A	ENSP00000392618.3	A0A1X7SBU6

Frequencies

GnomAD3 genomes AF: 0.589 AC: 89425 AN: 151854 Hom.: 26831 Cov.: 31

Gnomad AFR AF: 0.509

Gnomad AMI AF: 0.534

Gnomad AMR AF: 0.714

Gnomad ASJ AF: 0.500

Gnomad EAS AF: 0.829

Gnomad SAS AF: 0.692

Gnomad FIN AF: 0.622

Gnomad MID AF: 0.592

Gnomad NFE AF: 0.583

Gnomad OTH AF: 0.613

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

GnomAD4 genome AF: 0.589 AC: 89488 AN: 151972 Hom.: 26847 Cov.: 31 AF XY: 0.596 AC XY: 44295 AN XY: 74294

African (AFR) AF: 0.509 AC: 21102 AN: 41432

American (AMR) AF: 0.714 AC: 10905 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.500 AC: 1731 AN: 3464

East Asian (EAS) AF: 0.828 AC: 4266 AN: 5154

South Asian (SAS) AF: 0.692 AC: 3334 AN: 4820

European-Finnish (FIN) AF: 0.622 AC: 6572 AN: 10560

Middle Eastern (MID) AF: 0.599 AC: 176 AN: 294

European-Non Finnish (NFE) AF: 0.583 AC: 39615 AN: 67966

Other (OTH) AF: 0.618 AC: 1302 AN: 2108

Alfa AF: 0.585 Hom.: 4975

Bravo AF: 0.589

Asia WGS AF: 0.769 AC: 2672 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.025
DANN	Benign	0.37
PhyloP100		-1.9
Mutation Taster		=100/0	polymorphism (auto)

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs3098356;

hg19: chr5-90168011;

COSMIC: COSV67981264;