3-42525971-A-G
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBS1BS2
The NM_004624.4(VIPR1):c.377A>G(p.Asp126Gly) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00106 in 1,613,234 control chromosomes in the GnomAD database, including 32 homozygotes. In-silico tool predicts a benign outcome for this variant. 12/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.0010 ( 0 hom., cov: 32)
Exomes 𝑓: 0.0011 ( 32 hom. )
Consequence
VIPR1
NM_004624.4 missense
NM_004624.4 missense
Scores
2
14
Clinical Significance
Conservation
PhyloP100: 1.07
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]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -14 ACMG points.
BP4
?
Computational evidence support a benign effect (MetaRNN=0.0042209923).
BP6
?
Variant 3-42525971-A-G is Benign according to our data. Variant chr3-42525971-A-G is described in ClinVar as [Benign]. Clinvar id is 731807.Status of the report is criteria_provided_single_submitter, 1 stars.
BS1
?
Variant frequency is greater than expected in population eas. gnomad4 allele frequency = 0.000998 (152/152322) while in subpopulation EAS AF= 0.0211 (109/5166). AF 95% confidence interval is 0.0179. There are 0 homozygotes in gnomad4. There are 88 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
BS2
?
High Homozygotes in GnomAdExome at 5 gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
VIPR1 | NM_004624.4 | c.377A>G | p.Asp126Gly | missense_variant | 4/13 | ENST00000325123.5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
VIPR1 | ENST00000325123.5 | c.377A>G | p.Asp126Gly | missense_variant | 4/13 | 1 | NM_004624.4 | P4 | |
VIPR1-AS1 | ENST00000452639.7 | n.952+2578T>C | intron_variant, non_coding_transcript_variant | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.000999 AC: 152AN: 152204Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.00170 AC: 420AN: 247650Hom.: 5 AF XY: 0.00164 AC XY: 220AN XY: 134066
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GnomAD4 exome AF: 0.00106 AC: 1555AN: 1460912Hom.: 32 Cov.: 31 AF XY: 0.00107 AC XY: 775AN XY: 726592
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GnomAD4 genome ? AF: 0.000998 AC: 152AN: 152322Hom.: 0 Cov.: 32 AF XY: 0.00118 AC XY: 88AN XY: 74484
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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 submitter | clinical testing | Invitae | Dec 14, 2017 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
Cadd
Benign
Dann
Uncertain
Eigen
Benign
Eigen_PC
Benign
FATHMM_MKL
Benign
N
LIST_S2
Benign
T;T;T;T;T
MetaRNN
Benign
T;T;T;T;T
MetaSVM
Benign
T
MutationTaster
Benign
N;N;N;N
PrimateAI
Benign
T
PROVEAN
Uncertain
D;D;D;D;D
REVEL
Benign
Sift
Benign
T;T;T;D;T
Sift4G
Benign
T;T;T;T;T
Polyphen
0.33
.;.;.;.;B
Vest4
MVP
MPC
0.13
ClinPred
T
GERP RS
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gMVP
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at