chr3-42530054-C-T

Variant names:

• chr3-42530054-C-T
• rs417387
• NM_004624.4:c.637-725C>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.637-725C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.41 in 149,634 control chromosomes in the GnomAD database, including 12,880 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 0.41 (12863 hom., cov: 32)
  • Exomes 𝑓: 0.34 (17 hom.)
• Consequence: VIPR1 NM_004624.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.40
• Publications: 7 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=-0.8).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.553 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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	VIPR1	NM_004624.4	MANE Select	c.637-725C>T		intron	N/A	NP_004615.2
	VIPR1	NM_001251885.2		c.556-725C>T		intron	N/A	NP_001238814.1	B4DNY6
	VIPR1	NM_001251882.2		c.514-725C>T		intron	N/A	NP_001238811.1	P32241-5

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	VIPR1	ENST00000325123.5	TSL:1 MANE Select	c.637-725C>T		intron	N/A	ENSP00000327246.4	P32241-1
	VIPR1	ENST00000883021.1		c.667-725C>T		intron	N/A	ENSP00000553080.1
	VIPR1	ENST00000883016.1		c.634-725C>T		intron	N/A	ENSP00000553075.1

Frequencies

GnomAD3 genomes AF: 0.411 AC: 61268 AN: 149218 Hom.: 12865 Cov.: 32

Gnomad AFR AF: 0.291

Gnomad AMI AF: 0.348

Gnomad AMR AF: 0.444

Gnomad ASJ AF: 0.516

Gnomad EAS AF: 0.571

Gnomad SAS AF: 0.542

Gnomad FIN AF: 0.449

Gnomad MID AF: 0.487

Gnomad NFE AF: 0.440

Gnomad OTH AF: 0.425

GnomAD4 exome AF: 0.338 AC: 100 AN: 296 Hom.: 17 Cov.: 0 AF XY: 0.298 AC XY: 50 AN XY: 168

African (AFR) AF: 0.00 AC: 0 AN: 4

American (AMR) AF: 0.222 AC: 4 AN: 18

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AF: 0.333 AC: 2 AN: 6

European-Finnish (FIN) AF: 0.438 AC: 21 AN: 48

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.333 AC: 68 AN: 204

Other (OTH) AF: 0.313 AC: 5 AN: 16

GnomAD4 genome AF: 0.410 AC: 61284 AN: 149338 Hom.: 12863 Cov.: 32 AF XY: 0.413 AC XY: 30116 AN XY: 72938

African (AFR) AF: 0.291 AC: 11440 AN: 39302

American (AMR) AF: 0.444 AC: 6750 AN: 15210

Ashkenazi Jewish (ASJ) AF: 0.516 AC: 1786 AN: 3458

East Asian (EAS) AF: 0.571 AC: 2862 AN: 5016

South Asian (SAS) AF: 0.542 AC: 2572 AN: 4746

European-Finnish (FIN) AF: 0.449 AC: 4700 AN: 10474

Middle Eastern (MID) AF: 0.483 AC: 142 AN: 294

European-Non Finnish (NFE) AF: 0.440 AC: 29834 AN: 67848

Other (OTH) AF: 0.423 AC: 885 AN: 2090

Alfa AF: 0.426 Hom.: 2812

Bravo AF: 0.400

Asia WGS AF: 0.521 AC: 1816 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	5.4
DANN	Benign	0.34
PhyloP100		1.4
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: rs417387; hg19: chr3-42571546;