chr3-42509881-C-T

Position:

• chr3-42509881-C-T

Variant summary

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

The NM_004624.4(VIPR1):​c.79-3868C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.314 in 152,248 control chromosomes in the GnomAD database, including 9,044 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 0.31 (9032 hom., cov: 32)
  • Exomes 𝑓: 0.50 (12 hom.)
• Consequence: VIPR1 NM_004624.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.06

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=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.405 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
VIPR1	NM_004624.4	c.79-3868C>T		intron_variant		ENST00000325123.5	NP_004615.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
VIPR1	ENST00000325123.5	c.79-3868C>T		intron_variant		1	NM_004624.4	ENSP00000327246	P4
VIPR1-AS1	ENST00000452639.7	n.1242+2177G>A		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.314 AC: 47749 AN: 152026 Hom.: 9029 Cov.: 32

Gnomad AFR AF: 0.101

Gnomad AMI AF: 0.427

Gnomad AMR AF: 0.405

Gnomad ASJ AF: 0.419

Gnomad EAS AF: 0.143

Gnomad SAS AF: 0.254

Gnomad FIN AF: 0.463

Gnomad MID AF: 0.354

Gnomad NFE AF: 0.409

Gnomad OTH AF: 0.347

GnomAD4 exome AF: 0.500 AC: 52 AN: 104 Hom.: 12 AF XY: 0.515 AC XY: 34 AN XY: 66

Gnomad4 AFR exome AF: 0.250

Gnomad4 AMR exome AF: 0.500

Gnomad4 NFE exome AF: 0.547

Gnomad4 OTH exome AF: 0.250

GnomAD4 genome AF: 0.314 AC: 47769 AN: 152144 Hom.: 9032 Cov.: 32 AF XY: 0.316 AC XY: 23507 AN XY: 74368

Gnomad4 AFR AF: 0.101

Gnomad4 AMR AF: 0.406

Gnomad4 ASJ AF: 0.419

Gnomad4 EAS AF: 0.143

Gnomad4 SAS AF: 0.254

Gnomad4 FIN AF: 0.463

Gnomad4 NFE AF: 0.410

Gnomad4 OTH AF: 0.344

Alfa AF: 0.397 Hom.: 15130

Bravo AF: 0.301

Asia WGS AF: 0.226 AC: 787 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	0.59
DANN	Benign	0.26

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: rs7627240; hg19: chr3-42551373;