7-159028278-C-T

Variant names:

• chr7-159028278-C-T
• rs885863
• NM_003382.5:c.*2338G>A

Variant summary

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

The NM_003382.5(VIPR2):​c.*2338G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.438 in 154,596 control chromosomes in the GnomAD database, including 17,195 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 0.44 (16852 hom., cov: 35)
  • Exomes 𝑓: 0.51 (343 hom.)
• Consequence: VIPR2 NM_003382.5 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.00700

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 = 0.574 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
VIPR2	NM_003382.5	c.*2338G>A		3_prime_UTR_variant	Exon 13 of 13	ENST00000262178.7	NP_003373.2
VIPR2	NM_001308259.1	c.*2338G>A		3_prime_UTR_variant	Exon 10 of 10		NP_001295188.1
VIPR2	NM_001304522.2	c.*2338G>A		3_prime_UTR_variant	Exon 11 of 11		NP_001291451.1
VIPR2	NR_130758.2	n.4085G>A		non_coding_transcript_exon_variant	Exon 13 of 13

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
VIPR2	ENST00000262178	c.*2338G>A		3_prime_UTR_variant	Exon 13 of 13	1	NM_003382.5	ENSP00000262178.2
LINC00689	ENST00000413238.1	n.2767C>T		non_coding_transcript_exon_variant	Exon 4 of 4	1

Frequencies

GnomAD3 genomes AF: 0.436 AC: 66372 AN: 152062 Hom.: 16838 Cov.: 35

Gnomad AFR AF: 0.186

Gnomad AMI AF: 0.489

Gnomad AMR AF: 0.497

Gnomad ASJ AF: 0.575

Gnomad EAS AF: 0.172

Gnomad SAS AF: 0.429

Gnomad FIN AF: 0.493

Gnomad MID AF: 0.430

Gnomad NFE AF: 0.579

Gnomad OTH AF: 0.464

GnomAD4 exome AF: 0.510 AC: 1231 AN: 2416 Hom.: 343 Cov.: 0 AF XY: 0.511 AC XY: 639 AN XY: 1250

Gnomad4 AFR exome AF: 0.150

Gnomad4 AMR exome AF: 0.587

Gnomad4 ASJ exome AF: 0.518

Gnomad4 EAS exome AF: 0.174

Gnomad4 SAS exome AF: 0.467

Gnomad4 FIN exome AF: 0.492

Gnomad4 NFE exome AF: 0.581

Gnomad4 OTH exome AF: 0.500

GnomAD4 genome AF: 0.436 AC: 66411 AN: 152180 Hom.: 16852 Cov.: 35 AF XY: 0.429 AC XY: 31880 AN XY: 74392

Gnomad4 AFR AF: 0.186

Gnomad4 AMR AF: 0.498

Gnomad4 ASJ AF: 0.575

Gnomad4 EAS AF: 0.172

Gnomad4 SAS AF: 0.429

Gnomad4 FIN AF: 0.493

Gnomad4 NFE AF: 0.579

Gnomad4 OTH AF: 0.465

Alfa AF: 0.536 Hom.: 22537

Bravo AF: 0.429

Asia WGS AF: 0.296 AC: 1035 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	2.5
DANN	Benign	0.70

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: rs885863; hg19: chr7-158820969;