rs7105083
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Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_004621.6(TRPC6):c.2485-138C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.243 in 696,594 control chromosomes in the GnomAD database, including 24,924 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.31 ( 9617 hom., cov: 32)
Exomes 𝑓: 0.22 ( 15307 hom. )
Consequence
TRPC6
NM_004621.6 intron
NM_004621.6 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: -2.50
Genes affected
TRPC6 (HGNC:12338): (transient receptor potential cation channel subfamily C member 6) The protein encoded by this gene forms a receptor-activated calcium channel in the cell membrane. The channel is activated by diacylglycerol and is thought to be under the control of a phosphatidylinositol second messenger system. Activation of this channel occurs independently of protein kinase C and is not triggered by low levels of intracellular calcium. Defects in this gene are a cause of focal segmental glomerulosclerosis 2 (FSGS2). [provided by RefSeq, Mar 2009]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -14 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.99).
BP6
?
Variant 11-101455239-G-A is Benign according to our data. Variant chr11-101455239-G-A is described in ClinVar as [Benign]. Clinvar id is 1234385.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.575 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TRPC6 | NM_004621.6 | c.2485-138C>T | intron_variant | ENST00000344327.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TRPC6 | ENST00000344327.8 | c.2485-138C>T | intron_variant | 1 | NM_004621.6 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.311 AC: 47310AN: 151936Hom.: 9584 Cov.: 32
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GnomAD4 exome AF: 0.224 AC: 121871AN: 544540Hom.: 15307 Cov.: 7 AF XY: 0.224 AC XY: 65111AN XY: 290696
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GnomAD4 genome ? AF: 0.312 AC: 47399AN: 152054Hom.: 9617 Cov.: 32 AF XY: 0.304 AC XY: 22583AN XY: 74326
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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 | GeneDx | Aug 20, 2019 | - - |
Computational 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