12-813797-G-A
Variant summary
Our verdict is Benign. Variant got -17 ACMG points: 0P and 17B. BP4_StrongBP6_Very_StrongBP7BS2
The ENST00000315939.11(WNK1):c.915G>A(p.Thr305=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000709 in 1,613,790 control chromosomes in the GnomAD database, including 5 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. T305T) has been classified as Likely benign.
Frequency
Consequence
ENST00000315939.11 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -17 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
WNK1 | NM_213655.5 | c.915G>A | p.Thr305= | synonymous_variant | 2/28 | ENST00000340908.9 | NP_998820.3 | |
WNK1 | NM_018979.4 | c.915G>A | p.Thr305= | synonymous_variant | 2/28 | ENST00000315939.11 | NP_061852.3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
WNK1 | ENST00000340908.9 | c.915G>A | p.Thr305= | synonymous_variant | 2/28 | 5 | NM_213655.5 | ENSP00000341292 | A2 | |
WNK1 | ENST00000315939.11 | c.915G>A | p.Thr305= | synonymous_variant | 2/28 | 1 | NM_018979.4 | ENSP00000313059 | P2 |
Frequencies
GnomAD3 genomes AF: 0.000592 AC: 90AN: 152152Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000689 AC: 173AN: 251126Hom.: 0 AF XY: 0.000862 AC XY: 117AN XY: 135754
GnomAD4 exome AF: 0.000721 AC: 1054AN: 1461520Hom.: 5 Cov.: 32 AF XY: 0.000789 AC XY: 574AN XY: 727072
GnomAD4 genome AF: 0.000591 AC: 90AN: 152270Hom.: 0 Cov.: 32 AF XY: 0.000712 AC XY: 53AN XY: 74446
ClinVar
Submissions by phenotype
not provided Benign:3
Likely benign, criteria provided, single submitter | not provided | Breakthrough Genomics, Breakthrough Genomics | - | - - |
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Aug 01, 2024 | WNK1: BP4, BP7 - |
Likely benign, criteria provided, single submitter | clinical testing | ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories | Aug 18, 2023 | - - |
Pseudohypoaldosteronism type 2C;C2752089:Neuropathy, hereditary sensory and autonomic, type 2A Benign:2
Likely benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Jan 10, 2024 | - - |
Likely benign, criteria provided, single submitter | clinical testing | Fulgent Genetics, Fulgent Genetics | Dec 09, 2021 | - - |
Pseudohypoaldosteronism type 2C 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. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at