12-865160-G-C
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_213655.5(WNK1):c.2190G>C(p.Leu730Phe) variant causes a missense change. The variant allele was found at a frequency of 0.107 in 1,531,320 control chromosomes in the GnomAD database, including 9,260 homozygotes. In-silico tool predicts a benign outcome for this variant. 8/13 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
Genome browser will be placed here
ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
WNK1 | ENST00000340908.9 | c.2190G>C | p.Leu730Phe | missense_variant | Exon 9 of 28 | 5 | NM_213655.5 | ENSP00000341292.5 | ||
WNK1 | ENST00000315939.11 | c.2139+2890G>C | intron_variant | Intron 8 of 27 | 1 | NM_018979.4 | ENSP00000313059.6 |
Frequencies
GnomAD3 genomes AF: 0.114 AC: 16983AN: 149112Hom.: 1082 Cov.: 32
GnomAD3 exomes AF: 0.115 AC: 15132AN: 131620Hom.: 1002 AF XY: 0.110 AC XY: 7873AN XY: 71572
GnomAD4 exome AF: 0.106 AC: 146164AN: 1382090Hom.: 8174 Cov.: 40 AF XY: 0.104 AC XY: 71202AN XY: 681716
GnomAD4 genome AF: 0.114 AC: 17010AN: 149230Hom.: 1086 Cov.: 32 AF XY: 0.114 AC XY: 8259AN XY: 72740
ClinVar
Submissions by phenotype
not provided Benign:2
- -
This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. -
Pseudohypoaldosteronism type 2C;C2752089:Neuropathy, hereditary sensory and autonomic, type 2A Benign:1
- -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at