rs3821647
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Variant summary
Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP7BA1
The NM_001251845.2(TRPC1):c.2031G>A(p.Thr677=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.187 in 1,613,014 control chromosomes in the GnomAD database, including 28,740 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 0.19 ( 2813 hom., cov: 32)
Exomes 𝑓: 0.19 ( 25927 hom. )
Consequence
TRPC1
NM_001251845.2 synonymous
NM_001251845.2 synonymous
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -1.53
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 -13 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.49).
BP7
?
Synonymous conserved (PhyloP=-1.53 with no splicing effect.
BA1
?
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.256 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TRPC1 | NM_001251845.2 | c.2031G>A | p.Thr677= | synonymous_variant | 12/13 | ENST00000476941.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TRPC1 | ENST00000476941.6 | c.2031G>A | p.Thr677= | synonymous_variant | 12/13 | 1 | NM_001251845.2 | P1 | |
TRPC1 | ENST00000273482.10 | c.1929G>A | p.Thr643= | synonymous_variant | 11/12 | 1 | |||
TRPC1 | ENST00000698238.1 | c.2340G>A | p.Thr780= | synonymous_variant | 12/13 |
Frequencies
GnomAD3 genomes ? AF: 0.190 AC: 28847AN: 151866Hom.: 2808 Cov.: 32
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GnomAD3 exomes AF: 0.178 AC: 44754AN: 250810Hom.: 4327 AF XY: 0.176 AC XY: 23871AN XY: 135548
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GnomAD4 exome AF: 0.187 AC: 272543AN: 1461030Hom.: 25927 Cov.: 32 AF XY: 0.184 AC XY: 133614AN XY: 726822
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GnomAD4 genome ? AF: 0.190 AC: 28871AN: 151984Hom.: 2813 Cov.: 32 AF XY: 0.188 AC XY: 13988AN XY: 74256
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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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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at