Menu
GeneBe

3-42527470-C-T

Variant summary

Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_StrongBP6_ModerateBP7BS2

The NM_004624.4(VIPR1):c.477C>T(p.Val159=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00277 in 1,613,896 control chromosomes in the GnomAD database, including 34 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.0025 ( 2 hom., cov: 33)
Exomes 𝑓: 0.0028 ( 32 hom. )

Consequence

VIPR1
NM_004624.4 synonymous

Scores

2

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -2.04
Variant links:
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)

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -11 ACMG points.

BP4
?
    BP4 - Multiple lines of computational evidence suggest no impact on gene or gene product (conservation, evolutionary, splicing impact, etc.)
Computational evidence support a benign effect (BayesDel_noAF=-0.74).
BP6
?
    BP6 - Reputable source recently reports variant as benign, but the evidence is not available to the laboratory to perform an independent evaluation
Variant 3-42527470-C-T is Benign according to our data. Variant chr3-42527470-C-T is described in ClinVar as [Benign]. Clinvar id is 733479.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
    BP7 - A synonymous (silent) variant for which splicing prediction algorithms predict no impact to the splice consensus sequence nor the creation of a new splice site AND the nucleotide is not highly conserved
Synonymous conserved (PhyloP=-2.04 with no splicing effect.
BS2
?
    BS2 - Observed in a healthy adult individual for a recessive (homozygous), dominant (heterozygous), or X-linked (hemizygous) disorder, with full penetrance expected at an early age
High Homozygotes in GnomAd at 2 gene

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
VIPR1NM_004624.4 linkuse as main transcriptc.477C>T p.Val159= synonymous_variant 5/13 ENST00000325123.5

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
VIPR1ENST00000325123.5 linkuse as main transcriptc.477C>T p.Val159= synonymous_variant 5/131 NM_004624.4 P4P32241-1
VIPR1-AS1ENST00000452639.7 linkuse as main transcriptn.952+1079G>A intron_variant, non_coding_transcript_variant 5

Frequencies

GnomAD3 genomes
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.00250
AC:
381
AN:
152176
Hom.:
2
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.000579
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00412
Gnomad ASJ
AF:
0.0375
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00207
Gnomad FIN
AF:
0.000377
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.00213
Gnomad OTH
AF:
0.00239
GnomAD3 exomes
AF:
0.00342
AC:
860
AN:
251268
Hom.:
10
AF XY:
0.00338
AC XY:
459
AN XY:
135804
show subpopulations
Gnomad AFR exome
AF:
0.000308
Gnomad AMR exome
AF:
0.00113
Gnomad ASJ exome
AF:
0.0483
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.000686
Gnomad FIN exome
AF:
0.000977
Gnomad NFE exome
AF:
0.00228
Gnomad OTH exome
AF:
0.00456
GnomAD4 exome
AF:
0.00279
AC:
4082
AN:
1461602
Hom.:
32
Cov.:
33
AF XY:
0.00281
AC XY:
2043
AN XY:
727132
show subpopulations
Gnomad4 AFR exome
AF:
0.000568
Gnomad4 AMR exome
AF:
0.00105
Gnomad4 ASJ exome
AF:
0.0462
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.00112
Gnomad4 FIN exome
AF:
0.000883
Gnomad4 NFE exome
AF:
0.00215
Gnomad4 OTH exome
AF:
0.00457
GnomAD4 genome
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.00250
AC:
381
AN:
152294
Hom.:
2
Cov.:
33
AF XY:
0.00252
AC XY:
188
AN XY:
74464
show subpopulations
Gnomad4 AFR
AF:
0.000577
Gnomad4 AMR
AF:
0.00411
Gnomad4 ASJ
AF:
0.0375
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00207
Gnomad4 FIN
AF:
0.000377
Gnomad4 NFE
AF:
0.00213
Gnomad4 OTH
AF:
0.00237
Alfa
AF:
0.00507
Hom.:
6
Bravo
AF:
0.00235
Asia WGS
AF:
0.000577
AC:
2
AN:
3478
EpiCase
AF:
0.00294
EpiControl
AF:
0.00243

ClinVar

Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

not provided Benign:1
Benign, criteria provided, single submitterclinical testingInvitaeJan 09, 2018- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.74
Cadd
Benign
0.45
Dann
Benign
0.86

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: rs149397146; hg19: chr3-42568962; COSMIC: COSV57296339; COSMIC: COSV57296339; API