NM_004624.4:c.*1089C>T

Variant names:

• chr3-42537370-C-T
• rs9677
• NM_004624.4:c.*1089C>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.*1089C>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 0.391 in 152,016 control chromosomes in the GnomAD database, including 12,178 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 0.39 (12177 hom., cov: 32)
  • Exomes 𝑓: 0.40 (1 hom.)
• Consequence: VIPR1 NM_004624.4 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.255
• Publications: 9 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=-0.84).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.452 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
VIPR1	NM_004624.4	c.*1089C>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.*1089C>T		3_prime_UTR_variant	Exon 13 of 13	1	NM_004624.4	ENSP00000327246.4

Frequencies

GnomAD3 genomes AF: 0.391 AC: 59453 AN: 151878 Hom.: 12178 Cov.: 32

Gnomad AFR AF: 0.278

Gnomad AMI AF: 0.314

Gnomad AMR AF: 0.388

Gnomad ASJ AF: 0.498

Gnomad EAS AF: 0.326

Gnomad SAS AF: 0.394

Gnomad FIN AF: 0.414

Gnomad MID AF: 0.513

Gnomad NFE AF: 0.457

Gnomad OTH AF: 0.413

GnomAD4 exome AF: 0.400 AC: 8 AN: 20 Hom.: 1 Cov.: 0 AF XY: 0.300 AC XY: 3 AN XY: 10

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 0.500 AC: 1 AN: 2

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.250 AC: 3 AN: 12

Other (OTH) AF: 0.667 AC: 4 AN: 6

GnomAD4 genome AF: 0.391 AC: 59467 AN: 151996 Hom.: 12177 Cov.: 32 AF XY: 0.388 AC XY: 28847 AN XY: 74294

African (AFR) AF: 0.278 AC: 11538 AN: 41470

American (AMR) AF: 0.387 AC: 5922 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.498 AC: 1727 AN: 3466

East Asian (EAS) AF: 0.326 AC: 1686 AN: 5168

South Asian (SAS) AF: 0.394 AC: 1898 AN: 4812

European-Finnish (FIN) AF: 0.414 AC: 4369 AN: 10546

Middle Eastern (MID) AF: 0.531 AC: 156 AN: 294

European-Non Finnish (NFE) AF: 0.457 AC: 31023 AN: 67936

Other (OTH) AF: 0.409 AC: 862 AN: 2108

Alfa AF: 0.399 Hom.: 7334

Bravo AF: 0.384

Asia WGS AF: 0.383 AC: 1333 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	5.7
DANN	Benign	0.32
PhyloP100		0.26
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: rs9677; hg19: chr3-42578862;