rs885861

chr7-159028856-G-A

Variant summary

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

The NM_003382.5(VIPR2):c.*1760C>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 0.427 in 150,960 control chromosomes in the GnomAD database, including 16,399 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 0.43 (16372 hom., cov: 34)
  • Exomes 𝑓: 0.51 (27 hom.)
• Consequence: VIPR2 NM_003382.5 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.369

Genes affected

VIPR2 (HGNC:12695): (vasoactive intestinal peptide receptor 2) 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. [provided by RefSeq, Aug 2011]

LINC00689 (HGNC:27217): (long intergenic non-protein coding RNA 689)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.57 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
VIPR2	NM_003382.5	c.*1760C>T		3_prime_UTR_variant	13/13	ENST00000262178.7
VIPR2	NM_001304522.2	c.*1760C>T		3_prime_UTR_variant	11/11
VIPR2	NM_001308259.1	c.*1760C>T		3_prime_UTR_variant	10/10
VIPR2	NR_130758.2	n.3507C>T		non_coding_transcript_exon_variant	13/13

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
VIPR2	ENST00000262178.7	c.*1760C>T		3_prime_UTR_variant	13/13	1	NM_003382.5	P2
LINC00689	ENST00000413238.1	n.3345G>A		non_coding_transcript_exon_variant	4/4	1

Frequencies

GnomAD3 genomes AF: 0.427 AC: 64260 AN: 150646 Hom.: 16356 Cov.: 34

Gnomad AFR AF: 0.150

Gnomad AMI AF: 0.490

Gnomad AMR AF: 0.490

Gnomad ASJ AF: 0.574

Gnomad EAS AF: 0.153

Gnomad SAS AF: 0.430

Gnomad FIN AF: 0.500

Gnomad MID AF: 0.424

Gnomad NFE AF: 0.575

Gnomad OTH AF: 0.456

GnomAD4 exome AF: 0.505 AC: 101 AN: 200 Hom.: 27 Cov.: 0 AF XY: 0.465 AC XY: 67 AN XY: 144

Gnomad4 AFR exome AF: 0.200

Gnomad4 AMR exome AF: 0.500

Gnomad4 ASJ exome AF: 0.500

Gnomad4 EAS exome AF: 0.375

Gnomad4 SAS exome AF: 0.500

Gnomad4 FIN exome AF: 1.00

Gnomad4 NFE exome AF: 0.524

Gnomad4 OTH exome AF: 0.500

GnomAD4 genome AF: 0.426 AC: 64293 AN: 150760 Hom.: 16372 Cov.: 34 AF XY: 0.420 AC XY: 30946 AN XY: 73702

Gnomad4 AFR AF: 0.150

Gnomad4 AMR AF: 0.490

Gnomad4 ASJ AF: 0.574

Gnomad4 EAS AF: 0.153

Gnomad4 SAS AF: 0.430

Gnomad4 FIN AF: 0.500

Gnomad4 NFE AF: 0.575

Gnomad4 OTH AF: 0.457

Alfa AF: 0.542 Hom.: 22410

Bravo AF: 0.412

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
Cadd	Benign	3.4
Dann	Benign	0.84

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: rs885861; hg19: chr7-158821547;