chr7-159043113-G-A
Variant summary
Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_ModerateBP6_ModerateBP7BA1
The NM_003382.5(VIPR2):c.519C>T(p.Ala173=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00169 in 1,614,052 control chromosomes in the GnomAD database, including 79 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.0020 ( 8 hom., cov: 31)
Exomes 𝑓: 0.0017 ( 71 hom. )
Consequence
VIPR2
NM_003382.5 synonymous
NM_003382.5 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.730
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]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -13 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.41).
BP6
?
Variant 7-159043113-G-A is Benign according to our data. Variant chr7-159043113-G-A is described in ClinVar as [Benign]. Clinvar id is 782852.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
Synonymous conserved (PhyloP=0.73 with no splicing effect.
BA1
?
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.0504 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
VIPR2 | NM_003382.5 | c.519C>T | p.Ala173= | synonymous_variant | 6/13 | ENST00000262178.7 | |
VIPR2 | NM_001308259.1 | c.471C>T | p.Ala157= | synonymous_variant | 3/10 | ||
VIPR2 | NM_001304522.2 | c.358-6211C>T | intron_variant | ||||
VIPR2 | NR_130758.2 | n.615C>T | non_coding_transcript_exon_variant | 6/13 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
VIPR2 | ENST00000262178.7 | c.519C>T | p.Ala173= | synonymous_variant | 6/13 | 1 | NM_003382.5 | P2 | |
VIPR2 | ENST00000402066.5 | c.942C>T | p.Ala314= | synonymous_variant | 6/13 | 5 | A2 | ||
VIPR2 | ENST00000377633.7 | c.471C>T | p.Ala157= | synonymous_variant | 3/10 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.00200 AC: 304AN: 152118Hom.: 8 Cov.: 31
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GnomAD3 exomes AF: 0.00445 AC: 1118AN: 251346Hom.: 34 AF XY: 0.00409 AC XY: 555AN XY: 135860
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GnomAD4 exome AF: 0.00166 AC: 2421AN: 1461816Hom.: 71 Cov.: 32 AF XY: 0.00155 AC XY: 1127AN XY: 727202
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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 | Apr 10, 2018 | - - |
Computational scores
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Name
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BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at