NM_032119.4:c.18432+12535G>A

Variant names:

• chr5-91114875-G-A
• rs10942625
• NM_032119.4:c.18432+12535G>A

Variant summary

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

The NM_032119.4(ADGRV1):​c.18432+12535G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.527 in 151,932 control chromosomes in the GnomAD database, including 23,229 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 0.53 (23229 hom., cov: 31)
• Consequence: ADGRV1 NM_032119.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.149
• Publications: 2 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]

LUCAT1 (HGNC:48498): (lung cancer associated transcript 1)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.635 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ADGRV1	NM_032119.4	c.18432+12535G>A		intron_variant	Intron 87 of 89	ENST00000405460.9	NP_115495.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ADGRV1	ENST00000405460.9	c.18432+12535G>A		intron_variant	Intron 87 of 89	1	NM_032119.4	ENSP00000384582.2

Frequencies

GnomAD3 genomes AF: 0.527 AC: 79972 AN: 151812 Hom.: 23223 Cov.: 31

Gnomad AFR AF: 0.277

Gnomad AMI AF: 0.607

Gnomad AMR AF: 0.582

Gnomad ASJ AF: 0.520

Gnomad EAS AF: 0.416

Gnomad SAS AF: 0.588

Gnomad FIN AF: 0.718

Gnomad MID AF: 0.532

Gnomad NFE AF: 0.640

Gnomad OTH AF: 0.508

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

GnomAD4 genome AF: 0.527 AC: 80000 AN: 151932 Hom.: 23229 Cov.: 31 AF XY: 0.532 AC XY: 39474 AN XY: 74242

African (AFR) AF: 0.278 AC: 11499 AN: 41416

American (AMR) AF: 0.582 AC: 8893 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.520 AC: 1804 AN: 3470

East Asian (EAS) AF: 0.416 AC: 2139 AN: 5146

South Asian (SAS) AF: 0.589 AC: 2830 AN: 4806

European-Finnish (FIN) AF: 0.718 AC: 7575 AN: 10552

Middle Eastern (MID) AF: 0.517 AC: 151 AN: 292

European-Non Finnish (NFE) AF: 0.640 AC: 43498 AN: 67962

Other (OTH) AF: 0.502 AC: 1060 AN: 2112

Alfa AF: 0.541 Hom.: 4587

Bravo AF: 0.504

Asia WGS AF: 0.483 AC: 1681 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.2
DANN	Benign	0.51
PhyloP100		-0.15
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

Other links and lift over

dbSNP: rs10942625; hg19: chr5-90410692;