rs61736905
Variant summary
Our verdict is Benign. Variant got -19 ACMG points: 1P and 20B. PP2BP4_StrongBP6_Very_StrongBA1
The NM_213655.5(WNK1):āc.2081T>Cā(p.Ile694Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00297 in 1,614,092 control chromosomes in the GnomAD database, including 103 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (ā ā ).
Frequency
Consequence
NM_213655.5 missense
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 |
---|---|---|---|---|---|---|---|
WNK1 | NM_213655.5 | c.2081T>C | p.Ile694Thr | missense_variant | 8/28 | ENST00000340908.9 | |
WNK1 | NM_018979.4 | c.2081T>C | p.Ile694Thr | missense_variant | 8/28 | ENST00000315939.11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
WNK1 | ENST00000340908.9 | c.2081T>C | p.Ile694Thr | missense_variant | 8/28 | 5 | NM_213655.5 | A2 | |
WNK1 | ENST00000315939.11 | c.2081T>C | p.Ile694Thr | missense_variant | 8/28 | 1 | NM_018979.4 | P2 |
Frequencies
GnomAD3 genomes ? AF: 0.0151 AC: 2303AN: 152140Hom.: 59 Cov.: 32
GnomAD3 exomes AF: 0.00409 AC: 1028AN: 251330Hom.: 23 AF XY: 0.00304 AC XY: 413AN XY: 135826
GnomAD4 exome AF: 0.00170 AC: 2488AN: 1461834Hom.: 44 Cov.: 32 AF XY: 0.00149 AC XY: 1080AN XY: 727228
GnomAD4 genome ? AF: 0.0151 AC: 2303AN: 152258Hom.: 59 Cov.: 32 AF XY: 0.0148 AC XY: 1103AN XY: 74442
ClinVar
Submissions by phenotype
not provided Benign:2
Benign, criteria provided, single submitter | clinical testing | ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories | Aug 10, 2020 | - - |
Benign, criteria provided, single submitter | clinical testing | GeneDx | Jul 15, 2018 | - - |
not specified Benign:1
Benign, criteria provided, single submitter | clinical testing | Athena Diagnostics | Mar 24, 2020 | - - |
Pseudohypoaldosteronism type 2C Benign:1
Benign, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Jan 12, 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. - |
Pseudohypoaldosteronism type 2C;C2752089:Neuropathy, hereditary sensory and autonomic, type 2A Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 27, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at