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GeneBe

3-42525927-G-A

Variant summary

Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_StrongBP6_ModerateBP7BS1BS2

The NM_004624.4(VIPR1):c.333G>A(p.Thr111=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00314 in 1,613,520 control chromosomes in the GnomAD database, including 85 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.015 ( 36 hom., cov: 32)
Exomes 𝑓: 0.0019 ( 49 hom. )

Consequence

VIPR1
NM_004624.4 synonymous

Scores

2

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -3.51
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 -15 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=-0.78).
BP6
?
    BP6 - Reputable source recently reports variant as benign, but the evidence is not available to the laboratory to perform an independent evaluation
Variant 3-42525927-G-A is Benign according to our data. Variant chr3-42525927-G-A is described in ClinVar as [Benign]. Clinvar id is 767896.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=-3.51 with no splicing effect.
BS1
?
    BS1 - Allele frequency is greater than expected for disorder
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.0147 (2246/152322) while in subpopulation AFR AF= 0.0483 (2008/41566). AF 95% confidence interval is 0.0465. There are 36 homozygotes in gnomad4. There are 1059 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
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 35 gene

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
VIPR1NM_004624.4 linkuse as main transcriptc.333G>A p.Thr111= synonymous_variant 4/13 ENST00000325123.5

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
VIPR1ENST00000325123.5 linkuse as main transcriptc.333G>A p.Thr111= synonymous_variant 4/131 NM_004624.4 P4P32241-1
VIPR1-AS1ENST00000452639.7 linkuse as main transcriptn.952+2622C>T intron_variant, non_coding_transcript_variant 5

Frequencies

GnomAD3 genomes
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.0147
AC:
2233
AN:
152204
Hom.:
35
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.0483
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00726
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.0139
Gnomad SAS
AF:
0.000829
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00316
Gnomad NFE
AF:
0.000250
Gnomad OTH
AF:
0.0124
GnomAD3 exomes
AF:
0.00464
AC:
1154
AN:
248482
Hom.:
15
AF XY:
0.00340
AC XY:
458
AN XY:
134520
show subpopulations
Gnomad AFR exome
AF:
0.0463
Gnomad AMR exome
AF:
0.00349
Gnomad ASJ exome
AF:
0.00
Gnomad EAS exome
AF:
0.0128
Gnomad SAS exome
AF:
0.000264
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.000302
Gnomad OTH exome
AF:
0.00314
GnomAD4 exome
AF:
0.00193
AC:
2823
AN:
1461198
Hom.:
49
Cov.:
31
AF XY:
0.00166
AC XY:
1208
AN XY:
726832
show subpopulations
Gnomad4 AFR exome
AF:
0.0475
Gnomad4 AMR exome
AF:
0.00358
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.0157
Gnomad4 SAS exome
AF:
0.000337
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.000153
Gnomad4 OTH exome
AF:
0.00383
GnomAD4 genome
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.0147
AC:
2246
AN:
152322
Hom.:
36
Cov.:
32
AF XY:
0.0142
AC XY:
1059
AN XY:
74486
show subpopulations
Gnomad4 AFR
AF:
0.0483
Gnomad4 AMR
AF:
0.00719
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.0139
Gnomad4 SAS
AF:
0.000829
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.000250
Gnomad4 OTH
AF:
0.0161
Alfa
AF:
0.00767
Hom.:
13
Bravo
AF:
0.0167
Asia WGS
AF:
0.00433
AC:
15
AN:
3478
EpiCase
AF:
0.000491
EpiControl
AF:
0.000356

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 testingInvitaeDec 31, 2019- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.78
Cadd
Benign
0.48
Dann
Benign
0.89

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: rs34664814; hg19: chr3-42567419; API