3-42537370-C-T

Position:

• chr3-42537370-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.*1089C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.391 in 152,016 control chromosomes in the GnomAD database, including 12,178 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 0.39 (12177 hom., cov: 32)
  • Exomes 𝑓: 0.40 (1 hom.)
• Consequence: VIPR1 NM_004624.4 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.255

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 (HGNC:):

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 = 0.452 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
VIPR1	NM_004624.4	c.*1089C>T		3_prime_UTR_variant	13/13	ENST00000325123.5	NP_004615.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
VIPR1	ENST00000325123.5	c.*1089C>T		3_prime_UTR_variant	13/13	1	NM_004624.4	ENSP00000327246.4

Frequencies

GnomAD3 genomes AF: 0.391 AC: 59453 AN: 151878 Hom.: 12178 Cov.: 32

Gnomad AFR AF: 0.278

Gnomad AMI AF: 0.314

Gnomad AMR AF: 0.388

Gnomad ASJ AF: 0.498

Gnomad EAS AF: 0.326

Gnomad SAS AF: 0.394

Gnomad FIN AF: 0.414

Gnomad MID AF: 0.513

Gnomad NFE AF: 0.457

Gnomad OTH AF: 0.413

GnomAD4 exome AF: 0.400 AC: 8 AN: 20 Hom.: 1 Cov.: 0 AF XY: 0.300 AC XY: 3 AN XY: 10

Gnomad4 FIN exome AF: 0.500

Gnomad4 NFE exome AF: 0.250

Gnomad4 OTH exome AF: 0.667

GnomAD4 genome AF: 0.391 AC: 59467 AN: 151996 Hom.: 12177 Cov.: 32 AF XY: 0.388 AC XY: 28847 AN XY: 74294

Gnomad4 AFR AF: 0.278

Gnomad4 AMR AF: 0.387

Gnomad4 ASJ AF: 0.498

Gnomad4 EAS AF: 0.326

Gnomad4 SAS AF: 0.394

Gnomad4 FIN AF: 0.414

Gnomad4 NFE AF: 0.457

Gnomad4 OTH AF: 0.409

Alfa AF: 0.392 Hom.: 4165

Bravo AF: 0.384

Asia WGS AF: 0.383 AC: 1333 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	5.7
DANN	Benign	0.32

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: rs9677; hg19: chr3-42578862;