rs10501986
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Variant summary
Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP6_Very_StrongBA1
The NM_004621.6(TRPC6):c.171-20A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.438 in 1,608,228 control chromosomes in the GnomAD database, including 157,253 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Genomes: 𝑓 0.46 ( 16365 hom., cov: 32)
Exomes 𝑓: 0.44 ( 140888 hom. )
Consequence
TRPC6
NM_004621.6 intron
NM_004621.6 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.0830
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 -16 ACMG points.
BP6
?
Variant 11-101504818-T-C is Benign according to our data. Variant chr11-101504818-T-C is described in ClinVar as [Benign]. Clinvar id is 259456.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr11-101504818-T-C is described in Lovd as [Benign].
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.539 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TRPC6 | NM_004621.6 | c.171-20A>G | intron_variant | ENST00000344327.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TRPC6 | ENST00000344327.8 | c.171-20A>G | intron_variant | 1 | NM_004621.6 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.459 AC: 69695AN: 151916Hom.: 16348 Cov.: 32
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GnomAD3 exomes AF: 0.409 AC: 99636AN: 243324Hom.: 21418 AF XY: 0.410 AC XY: 54164AN XY: 132066
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GnomAD4 exome AF: 0.436 AC: 634767AN: 1456194Hom.: 140888 Cov.: 43 AF XY: 0.434 AC XY: 314619AN XY: 724200
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GnomAD4 genome ? AF: 0.459 AC: 69772AN: 152034Hom.: 16365 Cov.: 32 AF XY: 0.455 AC XY: 33810AN XY: 74306
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ClinVar
Significance: Benign
Submissions summary: Benign:5
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not specified Benign:2
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | - | - - |
Benign, criteria provided, single submitter | clinical testing | Unidad de Genómica Garrahan, Hospital de Pediatría Garrahan | Jul 15, 2024 | This variant is classified as Benign based on local population frequency. This variant was detected in 67% of patients studied in a panel designed for Epileptic and Developmental Encephalopathy and Progressive Myoclonus Epilepsy. Number of patients: 62. Only high quality variants are reported. - |
not provided Benign:2
Benign, criteria provided, single submitter | clinical testing | GeneDx | Aug 20, 2019 | - - |
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 31, 2024 | - - |
Focal segmental glomerulosclerosis 2 Benign:1
Benign, criteria provided, single submitter | clinical testing | Genome-Nilou Lab | Sep 10, 2021 | - - |
Computational scores
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Name
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BayesDel_noAF
Benign
CADD
Uncertain
DANN
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
DS_AG_spliceai
Position offset: -1
Find out detailed SpliceAI scores and Pangolin per-transcript scores at