rs417387

chr3-42530054-C-T

Variant summary

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

The NM_004624.4(VIPR1):c.637-725C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.41 in 149,634 control chromosomes in the GnomAD database, including 12,880 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 0.41 (12863 hom., cov: 32)
  • Exomes 𝑓: 0.34 (17 hom.)
• Consequence: VIPR1 NM_004624.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.40

Genes affected

VIPR1 (HGNC:12694): (vasoactive intestinal peptide receptor 1) 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. Several transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Oct 2011]

VIPR1-AS1 (HGNC:40610): (VIPR1 antisense RNA 1)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.553 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
VIPR1	NM_004624.4	c.637-725C>T		intron_variant		ENST00000325123.5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
VIPR1	ENST00000325123.5	c.637-725C>T		intron_variant		1	NM_004624.4	P4
VIPR1-AS1	ENST00000452639.7	n.842+806G>A		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.411 AC: 61268 AN: 149218 Hom.: 12865 Cov.: 32

Gnomad AFR AF: 0.291

Gnomad AMI AF: 0.348

Gnomad AMR AF: 0.444

Gnomad ASJ AF: 0.516

Gnomad EAS AF: 0.571

Gnomad SAS AF: 0.542

Gnomad FIN AF: 0.449

Gnomad MID AF: 0.487

Gnomad NFE AF: 0.440

Gnomad OTH AF: 0.425

GnomAD4 exome AF: 0.338 AC: 100 AN: 296 Hom.: 17 Cov.: 0 AF XY: 0.298 AC XY: 50 AN XY: 168

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.222

Gnomad4 SAS exome AF: 0.333

Gnomad4 FIN exome AF: 0.438

Gnomad4 NFE exome AF: 0.333

Gnomad4 OTH exome AF: 0.313

GnomAD4 genome AF: 0.410 AC: 61284 AN: 149338 Hom.: 12863 Cov.: 32 AF XY: 0.413 AC XY: 30116 AN XY: 72938

Gnomad4 AFR AF: 0.291

Gnomad4 AMR AF: 0.444

Gnomad4 ASJ AF: 0.516

Gnomad4 EAS AF: 0.571

Gnomad4 SAS AF: 0.542

Gnomad4 FIN AF: 0.449

Gnomad4 NFE AF: 0.440

Gnomad4 OTH AF: 0.423

Alfa AF: 0.426 Hom.: 2812

Bravo AF: 0.400

Asia WGS AF: 0.521 AC: 1816 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
Cadd	Benign	5.4
Dann	Benign	0.34

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: rs417387; hg19: chr3-42571546;