chr3-42505635-T-C

Variant names:

• chr3-42505635-T-C
• rs1876506
• NM_004624.4:c.78+2822T>C

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 2 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]

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_004624.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	VIPR1	NM_004624.4	MANE Select	c.78+2822T>C		intron	N/A	NP_004615.2
	VIPR1	NM_001251885.2		c.14+2851T>C		intron	N/A	NP_001238814.1
	VIPR1	NM_001251882.2		c.-244-7116T>C		intron	N/A	NP_001238811.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	VIPR1	ENST00000325123.5	TSL:1 MANE Select	c.78+2822T>C		intron	N/A	ENSP00000327246.4
	VIPR1	ENST00000433647.5	TSL:2	c.-244-7116T>C		intron	N/A	ENSP00000394950.1
	VIPR1	ENST00000543411.5	TSL:2	c.43+2822T>C		intron	N/A	ENSP00000445701.1

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

African (AFR) AF: 0.320 AC: 13280 AN: 41530

American (AMR) AF: 0.0507 AC: 775 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.0510 AC: 177 AN: 3472

East Asian (EAS) AF: 0.0709 AC: 367 AN: 5176

South Asian (SAS) AF: 0.0477 AC: 230 AN: 4824

European-Finnish (FIN) AF: 0.00970 AC: 103 AN: 10624

Middle Eastern (MID) AF: 0.0578 AC: 17 AN: 294

European-Non Finnish (NFE) AF: 0.00929 AC: 632 AN: 68012

Other (OTH) AF: 0.0814 AC: 172 AN: 2114

Alfa AF: 0.0327 Hom.: 1238

Bravo AF: 0.117

Asia WGS AF: 0.0630 AC: 218 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	3.0
DANN	Benign	0.74
PhyloP100		-0.88
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs1876506; hg19: chr3-42547127;