chr3-42505635-T-C

Position:

• chr3-42505635-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.78+2822T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.103 in 152,258 control chromosomes in the GnomAD database, including 2,240 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 0.10 (2240 hom., cov: 33)
• Consequence: VIPR1 NM_004624.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.878

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=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.315 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
VIPR1	NM_004624.4	c.78+2822T>C		intron_variant		ENST00000325123.5	NP_004615.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
VIPR1	ENST00000325123.5	c.78+2822T>C		intron_variant		1	NM_004624.4	ENSP00000327246	P4

Frequencies

GnomAD3 genomes AF: 0.103 AC: 15715 AN: 152140 Hom.: 2230 Cov.: 33

Gnomad AFR AF: 0.320

Gnomad AMI AF: 0.00110

Gnomad AMR AF: 0.0508

Gnomad ASJ AF: 0.0510

Gnomad EAS AF: 0.0707

Gnomad SAS AF: 0.0476

Gnomad FIN AF: 0.00970

Gnomad MID AF: 0.0601

Gnomad NFE AF: 0.00928

Gnomad OTH AF: 0.0817

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

GnomAD4 genome AF: 0.103 AC: 15754 AN: 152258 Hom.: 2240 Cov.: 33 AF XY: 0.0998 AC XY: 7429 AN XY: 74446

Gnomad4 AFR AF: 0.320

Gnomad4 AMR AF: 0.0507

Gnomad4 ASJ AF: 0.0510

Gnomad4 EAS AF: 0.0709

Gnomad4 SAS AF: 0.0477

Gnomad4 FIN AF: 0.00970

Gnomad4 NFE AF: 0.00929

Gnomad4 OTH AF: 0.0814

Alfa AF: 0.0251 Hom.: 508

Bravo AF: 0.117

Asia WGS AF: 0.0630 AC: 218 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	3.0
DANN	Benign	0.74

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: rs1876506; hg19: chr3-42547127;