chr13-37692234-A-G
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Variant summary
Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_StrongBP6_ModerateBP7BS1BS2
The NM_016179.4(TRPC4):āc.999T>Cā(p.Cys333=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00094 in 1,614,138 control chromosomes in the GnomAD database, including 20 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (ā ).
Frequency
Genomes: š 0.0052 ( 10 hom., cov: 33)
Exomes š: 0.00049 ( 10 hom. )
Consequence
TRPC4
NM_016179.4 synonymous
NM_016179.4 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 1.70
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 -15 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.53).
BP6
Variant 13-37692234-A-G is Benign according to our data. Variant chr13-37692234-A-G is described in ClinVar as [Benign]. Clinvar id is 787106.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
Synonymous conserved (PhyloP=1.7 with no splicing effect.
BS1
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.00525 (799/152266) while in subpopulation AFR AF= 0.0187 (775/41552). AF 95% confidence interval is 0.0176. There are 10 homozygotes in gnomad4. There are 373 alleles in male gnomad4 subpopulation. Median coverage is 33. This position pass quality control queck.
BS2
High AC in GnomAd4 at 799 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TRPC4 | NM_016179.4 | c.999T>C | p.Cys333= | synonymous_variant | 4/11 | ENST00000379705.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TRPC4 | ENST00000379705.8 | c.999T>C | p.Cys333= | synonymous_variant | 4/11 | 1 | NM_016179.4 | P4 |
Frequencies
GnomAD3 genomes AF: 0.00523 AC: 795AN: 152148Hom.: 10 Cov.: 33
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GnomAD3 exomes AF: 0.00138 AC: 346AN: 251366Hom.: 8 AF XY: 0.00107 AC XY: 146AN XY: 135850
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GnomAD4 exome AF: 0.000492 AC: 719AN: 1461872Hom.: 10 Cov.: 31 AF XY: 0.000410 AC XY: 298AN XY: 727234
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GnomAD4 genome AF: 0.00525 AC: 799AN: 152266Hom.: 10 Cov.: 33 AF XY: 0.00501 AC XY: 373AN XY: 74454
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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 | Feb 25, 2018 | - - |
Computational 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