rs34880640
Variant summary
Our verdict is Benign. Variant got -19 ACMG points: 1P and 20B. PP2BP4_StrongBP6_Very_StrongBS1BS2
The ENST00000315939.11(WNK1):c.446C>T(p.Ala149Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00142 in 1,586,632 control chromosomes in the GnomAD database, including 30 homozygotes. In-silico tool predicts a benign outcome for this variant. 15/20 in silico tools predict 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. A149A) has been classified as Likely benign.
Frequency
Consequence
ENST00000315939.11 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 | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
WNK1 | NM_213655.5 | c.446C>T | p.Ala149Val | missense_variant | 1/28 | ENST00000340908.9 | NP_998820.3 | |
WNK1 | NM_018979.4 | c.446C>T | p.Ala149Val | missense_variant | 1/28 | ENST00000315939.11 | NP_061852.3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
WNK1 | ENST00000340908.9 | c.446C>T | p.Ala149Val | missense_variant | 1/28 | 5 | NM_213655.5 | ENSP00000341292 | A2 | |
WNK1 | ENST00000315939.11 | c.446C>T | p.Ala149Val | missense_variant | 1/28 | 1 | NM_018979.4 | ENSP00000313059 | P2 |
Frequencies
GnomAD3 genomes AF: 0.00144 AC: 219AN: 152192Hom.: 1 Cov.: 33
GnomAD3 exomes AF: 0.00332 AC: 638AN: 191920Hom.: 6 AF XY: 0.00337 AC XY: 354AN XY: 104938
GnomAD4 exome AF: 0.00142 AC: 2031AN: 1434322Hom.: 29 Cov.: 94 AF XY: 0.00156 AC XY: 1113AN XY: 711426
GnomAD4 genome AF: 0.00143 AC: 218AN: 152310Hom.: 1 Cov.: 33 AF XY: 0.00165 AC XY: 123AN XY: 74482
ClinVar
Submissions by phenotype
Pseudohypoaldosteronism type 2C Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Apr 27, 2017 | This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). Publications were found based on this search. The evidence from the literature, in combination with allele frequency data from public databases where available, was sufficient to determine this variant is unlikely to cause disease. Therefore, this variant is classified as likely benign. - |
Pseudohypoaldosteronism type 2C;C2752089:Neuropathy, hereditary sensory and autonomic, type 2A Benign:1
Benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Jan 23, 2024 | - - |
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories | Sep 14, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at