3-42526948-C-T

Variant names:

• chr3-42526948-C-T
• rs437876
• NM_004624.4:c.400-445C>T

Variant summary

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

The NM_004624.4(VIPR1):​c.400-445C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.531 in 151,964 control chromosomes in the GnomAD database, including 24,326 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 0.53 (24326 hom., cov: 31)
• Consequence: VIPR1 NM_004624.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.00

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 (EAS) allele frequency at 95% confidence interval = 0.825 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
VIPR1	NM_004624.4	c.400-445C>T		intron_variant	Intron 4 of 12	ENST00000325123.5	NP_004615.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
VIPR1	ENST00000325123.5	c.400-445C>T		intron_variant	Intron 4 of 12	1	NM_004624.4	ENSP00000327246.4

Frequencies

GnomAD3 genomes AF: 0.531 AC: 80578 AN: 151844 Hom.: 24288 Cov.: 31

Gnomad AFR AF: 0.809

Gnomad AMI AF: 0.275

Gnomad AMR AF: 0.456

Gnomad ASJ AF: 0.463

Gnomad EAS AF: 0.845

Gnomad SAS AF: 0.638

Gnomad FIN AF: 0.369

Gnomad MID AF: 0.551

Gnomad NFE AF: 0.379

Gnomad OTH AF: 0.514

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.531 AC: 80662 AN: 151964 Hom.: 24326 Cov.: 31 AF XY: 0.532 AC XY: 39528 AN XY: 74274

Gnomad4 AFR AF: 0.809

Gnomad4 AMR AF: 0.455

Gnomad4 ASJ AF: 0.463

Gnomad4 EAS AF: 0.846

Gnomad4 SAS AF: 0.638

Gnomad4 FIN AF: 0.369

Gnomad4 NFE AF: 0.379

Gnomad4 OTH AF: 0.517

Alfa AF: 0.417 Hom.: 13749

Bravo AF: 0.552

Asia WGS AF: 0.718 AC: 2498 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	0.21
DANN	Benign	0.45

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		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: rs437876; hg19: chr3-42568440;