3-42536843-T-C

Variant summary

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

The NM_004624.4(VIPR1):c.*562T>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.643 in 152,150 control chromosomes in the GnomAD database, including 32,574 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 0.64 (32574 hom., cov: 33)
  • Exomes 𝑓: 0.50 (8 hom.)
  • Failed GnomAD Quality Control
• Consequence: VIPR1 NM_004624.4 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0700

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.809 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
VIPR1	NM_004624.4	c.*562T>C		3_prime_UTR_variant	13/13	ENST00000325123.5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
VIPR1	ENST00000325123.5	c.*562T>C		3_prime_UTR_variant	13/13	1	NM_004624.4	P4

Frequencies

GnomAD3 genomes AF: 0.643 AC: 97780 AN: 152034 Hom.: 32541 Cov.: 33

Gnomad AFR AF: 0.817

Gnomad AMI AF: 0.536

Gnomad AMR AF: 0.577

Gnomad ASJ AF: 0.623

Gnomad EAS AF: 0.768

Gnomad SAS AF: 0.688

Gnomad FIN AF: 0.577

Gnomad MID AF: 0.671

Gnomad NFE AF: 0.552

Gnomad OTH AF: 0.635

GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.500 AC: 34 AN: 68 Hom.: 8 Cov.: 0 AF XY: 0.447 AC XY: 17 AN XY: 38

Gnomad4 AFR exome AF: 0.250

Gnomad4 EAS exome AF: 1.00

Gnomad4 FIN exome AF: 0.750

Gnomad4 NFE exome AF: 0.480

Gnomad4 OTH exome AF: 0.500

GnomAD4 genome AF: 0.643 AC: 97863 AN: 152150 Hom.: 32574 Cov.: 33 AF XY: 0.644 AC XY: 47930 AN XY: 74372

Gnomad4 AFR AF: 0.817

Gnomad4 AMR AF: 0.576

Gnomad4 ASJ AF: 0.623

Gnomad4 EAS AF: 0.769

Gnomad4 SAS AF: 0.688

Gnomad4 FIN AF: 0.577

Gnomad4 NFE AF: 0.552

Gnomad4 OTH AF: 0.634

Alfa AF: 0.610 Hom.: 6982

Bravo AF: 0.651

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
Cadd	Benign	4.6
Dann	Benign	0.56

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: rs896; hg19: chr3-42578335;