rs199888777
Variant names:
Your query was ambiguous. Multiple possible variants found:
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001130698.2(TRPC3):c.2547+18G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000691 in 1,447,556 control chromosomes in the GnomAD database, with no homozygous occurrence. 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: not found (cov: 32)
Exomes 𝑓: 6.9e-7 ( 0 hom. )
Consequence
TRPC3
NM_001130698.2 intron
NM_001130698.2 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.407
Genes affected
TRPC3 (HGNC:12335): (transient receptor potential cation channel subfamily C member 3) 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 Likely_benign. Variant got -2 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.87).
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
TRPC3 | ENST00000379645.8 | c.2547+18G>T | intron_variant | Intron 10 of 11 | 1 | NM_001130698.2 | ENSP00000368966.3 | |||
TRPC3 | ENST00000264811.9 | c.2328+18G>T | intron_variant | Intron 9 of 10 | 1 | ENSP00000264811.5 | ||||
TRPC3 | ENST00000513531.1 | c.2163+18G>T | intron_variant | Intron 8 of 9 | 1 | ENSP00000426899.1 | ||||
TRPC3 | ENST00000506449.1 | n.*1555+18G>T | intron_variant | Intron 10 of 11 | 1 | ENSP00000423866.1 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 genomes
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32
GnomAD3 exomes AF: 0.00000401 AC: 1AN: 249220Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 134836
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GnomAD4 exome AF: 6.91e-7 AC: 1AN: 1447556Hom.: 0 Cov.: 28 AF XY: 0.00 AC XY: 0AN XY: 721078
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GnomAD4 genome Cov.: 32
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ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
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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