rs885863

Variant summary

Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong

The NM_003382.5(VIPR2):​c.*2338G>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 35)

Consequence

VIPR2
NM_003382.5 3_prime_UTR

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.00700
Variant links:
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)

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ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -2 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.87).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
VIPR2NM_003382.5 linkuse as main transcriptc.*2338G>C 3_prime_UTR_variant 13/13 ENST00000262178.7
VIPR2NM_001304522.2 linkuse as main transcriptc.*2338G>C 3_prime_UTR_variant 11/11
VIPR2NM_001308259.1 linkuse as main transcriptc.*2338G>C 3_prime_UTR_variant 10/10
VIPR2NR_130758.2 linkuse as main transcriptn.4085G>C non_coding_transcript_exon_variant 13/13

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
VIPR2ENST00000262178.7 linkuse as main transcriptc.*2338G>C 3_prime_UTR_variant 13/131 NM_003382.5 P2P41587-1
LINC00689ENST00000413238.1 linkuse as main transcriptn.2767C>G non_coding_transcript_exon_variant 4/41

Frequencies

GnomAD3 genomes
Cov.:
35
GnomAD4 exome
Cov.:
0
GnomAD4 genome
Cov.:
35

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.87
CADD
Benign
1.9
DANN
Benign
0.64

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

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs885863; hg19: chr7-158820969; API