3-42526948-C-T

Variant names:

• chr3-42526948-C-T
• rs437876
• NM_004624.4:c.400-445C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_004624.4(VIPR1):​c.400-445C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.531 in 151,964 control chromosomes in the GnomAD database, including 24,326 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 0.53 (24326 hom., cov: 31)
• Consequence: VIPR1 NM_004624.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.00
• Publications: 14 publications found

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

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.825 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
VIPR1	NM_004624.4	c.400-445C>T		intron_variant	Intron 4 of 12	ENST00000325123.5	NP_004615.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
VIPR1	ENST00000325123.5	c.400-445C>T		intron_variant	Intron 4 of 12	1	NM_004624.4	ENSP00000327246.4

Frequencies

GnomAD3 genomes AF: 0.531 AC: 80578 AN: 151844 Hom.: 24288 Cov.: 31

Gnomad AFR AF: 0.809

Gnomad AMI AF: 0.275

Gnomad AMR AF: 0.456

Gnomad ASJ AF: 0.463

Gnomad EAS AF: 0.845

Gnomad SAS AF: 0.638

Gnomad FIN AF: 0.369

Gnomad MID AF: 0.551

Gnomad NFE AF: 0.379

Gnomad OTH AF: 0.514

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

GnomAD4 genome AF: 0.531 AC: 80662 AN: 151964 Hom.: 24326 Cov.: 31 AF XY: 0.532 AC XY: 39528 AN XY: 74274

African (AFR) AF: 0.809 AC: 33526 AN: 41462

American (AMR) AF: 0.455 AC: 6952 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.463 AC: 1605 AN: 3470

East Asian (EAS) AF: 0.846 AC: 4351 AN: 5146

South Asian (SAS) AF: 0.638 AC: 3064 AN: 4806

European-Finnish (FIN) AF: 0.369 AC: 3898 AN: 10568

Middle Eastern (MID) AF: 0.554 AC: 163 AN: 294

European-Non Finnish (NFE) AF: 0.379 AC: 25763 AN: 67926

Other (OTH) AF: 0.517 AC: 1089 AN: 2106

Alfa AF: 0.434 Hom.: 19825

Bravo AF: 0.552

Asia WGS AF: 0.718 AC: 2498 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.21
DANN	Benign	0.45
PhyloP100		-2.0
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs437876; hg19: chr3-42568440;