rs6459928

Variant names:

• chr7-159135878-C-T
• rs6459928
• NM_003382.5:c.151+6568G>A

Variant summary

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

The NM_003382.5(VIPR2):​c.151+6568G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.201 in 152,020 control chromosomes in the GnomAD database, including 3,222 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 0.20 (3222 hom., cov: 32)
• Consequence: VIPR2 NM_003382.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.918
• Publications: 3 publications found

Genes affected

VIPR2 (HGNC:12695): (vasoactive intestinal peptide receptor 2) This gene encodes a receptor for vasoactive intestinal peptide, a small neuropeptide. Vasoactive intestinal peptide is involved in smooth muscle relaxation, exocrine and endocrine secretion, and water and ion flux in lung and intestinal epithelia. Its actions are effected through integral membrane receptors associated with a guanine nucleotide binding protein which activates adenylate cyclase. [provided by RefSeq, Aug 2011]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.244 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
VIPR2	NM_003382.5	c.151+6568G>A		intron_variant	Intron 2 of 12	ENST00000262178.7	NP_003373.2
VIPR2	NM_001304522.2	c.151+6568G>A		intron_variant	Intron 2 of 10		NP_001291451.1
VIPR2	NR_130758.2	n.247+6568G>A		intron_variant	Intron 2 of 12

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
VIPR2	ENST00000262178.7	c.151+6568G>A		intron_variant	Intron 2 of 12	1	NM_003382.5	ENSP00000262178.2
VIPR2	ENST00000402066.5	c.574+6568G>A		intron_variant	Intron 2 of 12	5		ENSP00000384497.1
VIPR2	ENST00000421760.2	c.151+6568G>A		intron_variant	Intron 2 of 2	3		ENSP00000402690.2

Frequencies

GnomAD3 genomes AF: 0.201 AC: 30547 AN: 151902 Hom.: 3212 Cov.: 32

Gnomad AFR AF: 0.248

Gnomad AMI AF: 0.261

Gnomad AMR AF: 0.155

Gnomad ASJ AF: 0.124

Gnomad EAS AF: 0.179

Gnomad SAS AF: 0.182

Gnomad FIN AF: 0.214

Gnomad MID AF: 0.127

Gnomad NFE AF: 0.188

Gnomad OTH AF: 0.180

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

GnomAD4 genome AF: 0.201 AC: 30579 AN: 152020 Hom.: 3222 Cov.: 32 AF XY: 0.202 AC XY: 15009 AN XY: 74306

African (AFR) AF: 0.248 AC: 10281 AN: 41448

American (AMR) AF: 0.155 AC: 2365 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.124 AC: 430 AN: 3466

East Asian (EAS) AF: 0.179 AC: 925 AN: 5164

South Asian (SAS) AF: 0.182 AC: 876 AN: 4814

European-Finnish (FIN) AF: 0.214 AC: 2261 AN: 10572

Middle Eastern (MID) AF: 0.126 AC: 37 AN: 294

European-Non Finnish (NFE) AF: 0.188 AC: 12794 AN: 67964

Other (OTH) AF: 0.177 AC: 373 AN: 2110

Alfa AF: 0.193 Hom.: 5173

Bravo AF: 0.201

Asia WGS AF: 0.164 AC: 570 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	1.2
DANN	Benign	0.67
PhyloP100		-0.92
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: rs6459928; hg19: chr7-158928569;