rs145077205
Variant summary
Our verdict is Benign. Variant got -19 ACMG points: 0P and 19B. BP4_ModerateBP6_Very_StrongBP7BS1BS2
The NM_004621.6(TRPC6):c.2142G>T(p.Thr714=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00524 in 1,612,764 control chromosomes in the GnomAD database, including 54 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★). Synonymous variant affecting the same amino acid position (i.e. T714T) has been classified as Likely benign.
Frequency
Consequence
NM_004621.6 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -19 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TRPC6 | NM_004621.6 | c.2142G>T | p.Thr714= | synonymous_variant | 8/13 | ENST00000344327.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TRPC6 | ENST00000344327.8 | c.2142G>T | p.Thr714= | synonymous_variant | 8/13 | 1 | NM_004621.6 | P1 | |
TRPC6 | ENST00000360497.4 | c.1977G>T | p.Thr659= | synonymous_variant | 7/12 | 1 | |||
TRPC6 | ENST00000348423.8 | c.1794G>T | p.Thr598= | synonymous_variant | 6/11 | 1 | |||
TRPC6 | ENST00000532133.5 | c.1908G>T | p.Thr636= | synonymous_variant | 7/12 | 5 |
Frequencies
GnomAD3 genomes AF: 0.00407 AC: 619AN: 152090Hom.: 3 Cov.: 32
GnomAD3 exomes AF: 0.00581 AC: 1455AN: 250504Hom.: 10 AF XY: 0.00715 AC XY: 968AN XY: 135410
GnomAD4 exome AF: 0.00536 AC: 7828AN: 1460556Hom.: 51 Cov.: 31 AF XY: 0.00594 AC XY: 4313AN XY: 726616
GnomAD4 genome AF: 0.00405 AC: 616AN: 152208Hom.: 3 Cov.: 32 AF XY: 0.00415 AC XY: 309AN XY: 74402
ClinVar
Submissions by phenotype
not specified Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | - | - - |
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 15, 2024 | - - |
Focal segmental glomerulosclerosis Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Genome Diagnostics Laboratory, The Hospital for Sick Children | Sep 06, 2022 | - - |
Focal segmental glomerulosclerosis 2 Benign:1
Benign, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Jan 13, 2018 | This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease. - |
Prednisolone response Other:1
drug response, no assertion criteria provided | research | Genetic Testing Lab, Ashok and Rita Patel Institute of Integrated Study and Research in Biotechnology and Allied Sciences | Jan 18, 2016 | - sensitive to standard corticosteroid therapy |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at