3-42537087-A-T

Variant names:

• chr3-42537087-A-T
• rs14380
• NM_004624.4:c.*806A>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.*806A>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.246 in 152,068 control chromosomes in the GnomAD database, including 5,197 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 0.25 (5196 hom., cov: 32)
  • Exomes 𝑓: 0.20 (1 hom.)
• Consequence: VIPR1 NM_004624.4 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.755
• Publications: 6 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=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.38 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
VIPR1	NM_004624.4	c.*806A>T		3_prime_UTR_variant	Exon 13 of 13	ENST00000325123.5	NP_004615.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
VIPR1	ENST00000325123.5	c.*806A>T		3_prime_UTR_variant	Exon 13 of 13	1	NM_004624.4	ENSP00000327246.4

Frequencies

GnomAD3 genomes AF: 0.246 AC: 37329 AN: 151904 Hom.: 5197 Cov.: 32

Gnomad AFR AF: 0.365

Gnomad AMI AF: 0.132

Gnomad AMR AF: 0.256

Gnomad ASJ AF: 0.225

Gnomad EAS AF: 0.394

Gnomad SAS AF: 0.281

Gnomad FIN AF: 0.203

Gnomad MID AF: 0.192

Gnomad NFE AF: 0.166

Gnomad OTH AF: 0.248

GnomAD4 exome AF: 0.196 AC: 9 AN: 46 Hom.: 1 Cov.: 0 AF XY: 0.156 AC XY: 5 AN XY: 32

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 2

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 0.250 AC: 4 AN: 16

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.208 AC: 5 AN: 24

Other (OTH) AF: 0.00 AC: 0 AN: 4

GnomAD4 genome AF: 0.246 AC: 37358 AN: 152022 Hom.: 5196 Cov.: 32 AF XY: 0.250 AC XY: 18586 AN XY: 74310

African (AFR) AF: 0.365 AC: 15120 AN: 41438

American (AMR) AF: 0.257 AC: 3921 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.225 AC: 781 AN: 3466

East Asian (EAS) AF: 0.394 AC: 2031 AN: 5152

South Asian (SAS) AF: 0.280 AC: 1351 AN: 4820

European-Finnish (FIN) AF: 0.203 AC: 2149 AN: 10568

Middle Eastern (MID) AF: 0.193 AC: 56 AN: 290

European-Non Finnish (NFE) AF: 0.166 AC: 11302 AN: 67984

Other (OTH) AF: 0.250 AC: 527 AN: 2112

Alfa AF: 0.211 Hom.: 530

Bravo AF: 0.257

Asia WGS AF: 0.311 AC: 1081 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	5.0
DANN	Benign	0.50
PhyloP100		0.76
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: rs14380; hg19: chr3-42578579;