Variant 7-159032034-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -17 ACMG points: 0P and 17B. BP4_StrongBP6_Very_StrongBP7BS2

The NM_003382.5(VIPR2):c.1005G>A(p.Pro335Pro) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00634 in 1,614,058 control chromosomes in the GnomAD database, including 50 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).

Frequency

Genomes: 𝑓 0.0036 ( 3 hom., cov: 33)

Exomes 𝑓: 0.0066 ( 47 hom. )

Consequence

VIPR2
NM_003382.5 synonymous

Scores

Clinical Significance

Benign/Likely benign criteria provided, multiple submitters, no conflicts B:3

Conservation

PhyloP100: -7.20

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]

VIPR2 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -17 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.7).

BP6

Variant 7-159032034-C-T is Benign according to our data. Variant chr7-159032034-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 710208.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BP7

Synonymous conserved (PhyloP=-7.2 with no splicing effect.

BS2

High Homozygotes in GnomAd4 at 3 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
VIPR2	NM_003382.5 link	c.1005G>A	p.Pro335Pro	synonymous_variant	11/13	ENST00000262178.7	NP_003373.2	P41587-1X5D7Q6
VIPR2	NM_001308259.1 link	c.957G>A	p.Pro319Pro	synonymous_variant	8/10		NP_001295188.1	P41587-2
VIPR2	NM_001304522.2 link	c.765G>A	p.Pro255Pro	synonymous_variant	9/11		NP_001291451.1	P41587X5DP12
VIPR2	NR_130758.2 link	n.1101G>A		non_coding_transcript_exon_variant	11/13

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	UniProt
VIPR2	ENST00000262178.7 link	c.1005G>A	p.Pro335Pro	synonymous_variant	11/13	1	NM_003382.5	ENSP00000262178.2	P41587-1
VIPR2	ENST00000402066.5 link	c.1428G>A	p.Pro476Pro	synonymous_variant	11/13	5		ENSP00000384497.1	C9JCP7
VIPR2	ENST00000377633.7 link	c.957G>A	p.Pro319Pro	synonymous_variant	8/10	2		ENSP00000366860.3	P41587-2

Frequencies

GnomAD3 genomes

AF:

0.00364

AC:

554

AN:

152162

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00147

Gnomad AMI

AF:

0.00110

Gnomad AMR

AF:

0.00353

Gnomad ASJ

AF:

0.00259

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00124

Gnomad FIN

AF:

0.000283

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.00603

Gnomad OTH

AF:

0.00478

GnomAD3 exomes

AF:

0.00391

AC:

981

AN:

251146

Hom.:

AF XY:

0.00408

AC XY:

554

AN XY:

135842

show subpopulations

Gnomad AFR exome

AF:

0.00154

Gnomad AMR exome

AF:

0.00428

Gnomad ASJ exome

AF:

0.00288

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.00134

Gnomad FIN exome

AF:

0.000739

Gnomad NFE exome

AF:

0.00611

Gnomad OTH exome

AF:

0.00474

GnomAD4 exome

AF:

0.00662

AC:

9675

AN:

1461778

Hom.:

Cov.:

AF XY:

0.00651

AC XY:

4731

AN XY:

727182

show subpopulations

Gnomad4 AFR exome

AF:

0.00116

Gnomad4 AMR exome

AF:

0.00396

Gnomad4 ASJ exome

AF:

0.00245

Gnomad4 EAS exome

AF:

0.0000252

Gnomad4 SAS exome

AF:

0.00141

Gnomad4 FIN exome

AF:

0.000675

Gnomad4 NFE exome

AF:

0.00793

Gnomad4 OTH exome

AF:

0.00661

GnomAD4 genome

AF:

0.00364

AC:

554

AN:

152280

Hom.:

Cov.:

AF XY:

0.00321

AC XY:

239

AN XY:

74464

show subpopulations

Gnomad4 AFR

AF:

0.00147

Gnomad4 AMR

AF:

0.00353

Gnomad4 ASJ

AF:

0.00259

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00124

Gnomad4 FIN

AF:

0.000283

Gnomad4 NFE

AF:

0.00603

Gnomad4 OTH

AF:

0.00473

Alfa

AF:

0.00463

Hom.:

Bravo

AF:

0.00416

EpiCase

AF:

0.00649

EpiControl

AF:

0.00670

ClinVar

Significance: Benign/Likely benign

Submissions summary: Benign:3

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:3

Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Feb 13, 2018	- -
Likely benign, criteria provided, single submitter	clinical testing	CeGaT Center for Human Genetics Tuebingen	Jan 01, 2024	VIPR2: BP4, BP7, BS2 -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.70

CADD

Benign

0.24

DANN

Benign

0.91

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.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over