chr13-37636794-C-T
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_016179.4(TRPC4):c.*109G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.225 in 1,333,458 control chromosomes in the GnomAD database, including 37,396 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 0.22 ( 4338 hom., cov: 32)
Exomes 𝑓: 0.23 ( 33058 hom. )
Consequence
TRPC4
NM_016179.4 3_prime_UTR
NM_016179.4 3_prime_UTR
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.0830
Genes affected
TRPC4 (HGNC:12336): (transient receptor potential cation channel subfamily C member 4) This gene encodes a member of the canonical subfamily of transient receptor potential cation channels. The encoded protein forms a non-selective calcium-permeable cation channel that is activated by Gq-coupled receptors and tyrosine kinases, and plays a role in multiple processes including endothelial permeability, vasodilation, neurotransmitter release and cell proliferation. Single nucleotide polymorphisms in this gene may be associated with generalized epilepsy with photosensitivity. Alternatively spliced transcript variants encoding multiple isoforms have been observed for this gene. [provided by RefSeq, Aug 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=-0.64).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.665 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TRPC4 | NM_016179.4 | c.*109G>A | 3_prime_UTR_variant | 11/11 | ENST00000379705.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TRPC4 | ENST00000379705.8 | c.*109G>A | 3_prime_UTR_variant | 11/11 | 1 | NM_016179.4 | P4 |
Frequencies
GnomAD3 genomes AF: 0.224 AC: 33287AN: 148300Hom.: 4336 Cov.: 32
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GnomAD4 exome AF: 0.225 AC: 266937AN: 1185040Hom.: 33058 Cov.: 19 AF XY: 0.226 AC XY: 131532AN XY: 581228
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GnomAD4 genome AF: 0.224 AC: 33307AN: 148418Hom.: 4338 Cov.: 32 AF XY: 0.234 AC XY: 16988AN XY: 72532
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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