rs12828016
Variant summary
Our verdict is Benign. Variant got -19 ACMG points: 1P and 20B. PP2BP4_StrongBP6_Very_StrongBA1
The NM_213655.5(WNK1):c.6180G>T(p.Met2060Ile) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.388 in 1,612,936 control chromosomes in the GnomAD database, including 123,394 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 (★★).
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.6180G>T | p.Met2060Ile | missense_variant | 21/28 | ENST00000340908.9 | |
WNK1 | NM_018979.4 | c.5424G>T | p.Met1808Ile | missense_variant | 21/28 | ENST00000315939.11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
WNK1 | ENST00000340908.9 | c.6180G>T | p.Met2060Ile | missense_variant | 21/28 | 5 | NM_213655.5 | A2 | |
WNK1 | ENST00000315939.11 | c.5424G>T | p.Met1808Ile | missense_variant | 21/28 | 1 | NM_018979.4 | P2 |
Frequencies
GnomAD3 genomes ? AF: 0.407 AC: 61765AN: 151874Hom.: 13054 Cov.: 32
GnomAD3 exomes AF: 0.370 AC: 92947AN: 251292Hom.: 18022 AF XY: 0.375 AC XY: 50881AN XY: 135802
GnomAD4 exome AF: 0.386 AC: 563448AN: 1460944Hom.: 110328 Cov.: 39 AF XY: 0.388 AC XY: 281819AN XY: 726856
GnomAD4 genome ? AF: 0.407 AC: 61814AN: 151992Hom.: 13066 Cov.: 32 AF XY: 0.401 AC XY: 29825AN XY: 74302
ClinVar
Submissions by phenotype
not specified Benign:3
Benign, no assertion criteria provided | clinical testing | Joint Genome Diagnostic Labs from Nijmegen and Maastricht, Radboudumc and MUMC+ | - | - - |
Benign, no assertion criteria provided | clinical testing | Clinical Genetics, Academic Medical Center | - | - - |
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | - | - - |
Neuropathy, hereditary sensory and autonomic, type 2A Benign:2
Benign, criteria provided, single submitter | clinical testing | Athena Diagnostics | Jun 12, 2017 | - - |
Benign, criteria provided, single submitter | clinical testing | Genome-Nilou Lab | Jul 14, 2021 | - - |
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 | Feb 01, 2024 | - - |
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | Mar 03, 2015 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at