chr3-42525981-G-A
Variant summary
Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_StrongBP6_ModerateBP7BA1
The NM_004624.4(VIPR1):c.387G>A(p.Ala129=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00303 in 1,611,760 control chromosomes in the GnomAD database, including 135 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.016 ( 70 hom., cov: 32)
Exomes 𝑓: 0.0016 ( 65 hom. )
Consequence
VIPR1
NM_004624.4 synonymous
NM_004624.4 synonymous
Scores
1
12
Clinical Significance
Conservation
PhyloP100: -1.57
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 -15 ACMG points.
BP4
?
Computational evidence support a benign effect (MetaRNN=0.0025151372).
BP6
?
Variant 3-42525981-G-A is Benign according to our data. Variant chr3-42525981-G-A is described in ClinVar as [Benign]. Clinvar id is 787782.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
Synonymous conserved (PhyloP=-1.57 with no splicing effect.
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0538 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
VIPR1 | NM_004624.4 | c.387G>A | p.Ala129= | synonymous_variant | 4/13 | ENST00000325123.5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
VIPR1 | ENST00000325123.5 | c.387G>A | p.Ala129= | synonymous_variant | 4/13 | 1 | NM_004624.4 | P4 | |
VIPR1-AS1 | ENST00000452639.7 | n.952+2568C>T | intron_variant, non_coding_transcript_variant | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.0163 AC: 2485AN: 152204Hom.: 70 Cov.: 32
GnomAD3 genomes
?
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GnomAD3 exomes AF: 0.00394 AC: 963AN: 244164Hom.: 30 AF XY: 0.00299 AC XY: 395AN XY: 132232
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GnomAD4 exome AF: 0.00164 AC: 2393AN: 1459438Hom.: 65 Cov.: 30 AF XY: 0.00138 AC XY: 1005AN XY: 725660
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GnomAD4 genome ? AF: 0.0163 AC: 2490AN: 152322Hom.: 70 Cov.: 32 AF XY: 0.0160 AC XY: 1189AN XY: 74488
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ESP6500AA
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223
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ExAC
?
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591
Asia WGS
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14
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3478
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 | Apr 16, 2018 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
Cadd
Benign
Dann
Uncertain
Eigen
Benign
Eigen_PC
Benign
FATHMM_MKL
Benign
N
LIST_S2
Benign
T
MetaRNN
Benign
T
MetaSVM
Benign
T
MutationTaster
Benign
N;N;N;N
PROVEAN
Benign
N
REVEL
Benign
Sift
Benign
T
Vest4
MVP
ClinPred
T
GERP RS
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