chr3-42511624-A-G

Position:

• chr3-42511624-A-G

Variant summary

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

The NM_004624.4(VIPR1):​c.79-2125A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.809 in 151,886 control chromosomes in the GnomAD database, including 49,810 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 0.81 (49789 hom., cov: 32)
  • Exomes 𝑓: 0.90 (21 hom.)
• Consequence: VIPR1 NM_004624.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.11

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=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.963 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
VIPR1	NM_004624.4	c.79-2125A>G		intron_variant		ENST00000325123.5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
VIPR1	ENST00000325123.5	c.79-2125A>G		intron_variant		1	NM_004624.4	P4
VIPR1-AS1	ENST00000452639.7	n.1242+434T>C		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.809 AC: 122749 AN: 151714 Hom.: 49740 Cov.: 32

Gnomad AFR AF: 0.825

Gnomad AMI AF: 0.773

Gnomad AMR AF: 0.862

Gnomad ASJ AF: 0.812

Gnomad EAS AF: 0.986

Gnomad SAS AF: 0.839

Gnomad FIN AF: 0.751

Gnomad MID AF: 0.796

Gnomad NFE AF: 0.780

Gnomad OTH AF: 0.833

GnomAD4 exome AF: 0.904 AC: 47 AN: 52 Hom.: 21 AF XY: 0.875 AC XY: 28 AN XY: 32

Gnomad4 EAS exome AF: 1.00

Gnomad4 FIN exome AF: 0.875

Gnomad4 NFE exome AF: 0.933

Gnomad4 OTH exome AF: 0.833

GnomAD4 genome AF: 0.809 AC: 122857 AN: 151834 Hom.: 49789 Cov.: 32 AF XY: 0.809 AC XY: 60051 AN XY: 74208

Gnomad4 AFR AF: 0.825

Gnomad4 AMR AF: 0.862

Gnomad4 ASJ AF: 0.812

Gnomad4 EAS AF: 0.985

Gnomad4 SAS AF: 0.839

Gnomad4 FIN AF: 0.751

Gnomad4 NFE AF: 0.780

Gnomad4 OTH AF: 0.834

Alfa AF: 0.789 Hom.: 6749

Bravo AF: 0.822

Asia WGS AF: 0.914 AC: 3180 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.84
DANN	Benign	0.58

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: rs421558; hg19: chr3-42553116;