rs4259003
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_001251845.2(TRPC1):c.2154+83G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.213 in 1,331,468 control chromosomes in the GnomAD database, including 37,072 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.31 ( 10321 hom., cov: 32)
Exomes 𝑓: 0.20 ( 26751 hom. )
Consequence
TRPC1
NM_001251845.2 intron
NM_001251845.2 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.144
Genes affected
TRPC1 (HGNC:12333): (transient receptor potential cation channel subfamily C member 1) The protein encoded by this gene is a membrane protein that can form a non-selective channel permeable to calcium and other cations. The encoded protein appears to be induced to form channels by a receptor tyrosine kinase-activated phosphatidylinositol second messenger system and also by depletion of intracellular calcium stores. Two 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 -12 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.89).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.625 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TRPC1 | NM_001251845.2 | c.2154+83G>A | intron_variant | ENST00000476941.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TRPC1 | ENST00000476941.6 | c.2154+83G>A | intron_variant | 1 | NM_001251845.2 | P1 | |||
TRPC1 | ENST00000273482.10 | c.2052+83G>A | intron_variant | 1 | |||||
TRPC1 | ENST00000698238.1 | c.2463+83G>A | intron_variant |
Frequencies
GnomAD3 genomes AF: 0.311 AC: 47197AN: 151936Hom.: 10302 Cov.: 32
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GnomAD4 exome AF: 0.200 AC: 236058AN: 1179414Hom.: 26751 AF XY: 0.196 AC XY: 115462AN XY: 588312
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GnomAD4 genome AF: 0.311 AC: 47257AN: 152054Hom.: 10321 Cov.: 32 AF XY: 0.305 AC XY: 22644AN XY: 74328
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ClinVar
Not reported inComputational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
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