chr12-753950-G-A
Variant summary
Our verdict is Likely benign. Variant got -1 ACMG points: 1P and 2B. PP2BP4_Moderate
The NM_213655.5(WNK1):c.385G>A(p.Ala129Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000414 in 1,451,018 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. A129S) has been classified as Uncertain significance.
Frequency
Consequence
NM_213655.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
WNK1 | NM_213655.5 | c.385G>A | p.Ala129Thr | missense_variant | 1/28 | ENST00000340908.9 | |
WNK1 | NM_018979.4 | c.385G>A | p.Ala129Thr | missense_variant | 1/28 | ENST00000315939.11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
WNK1 | ENST00000340908.9 | c.385G>A | p.Ala129Thr | missense_variant | 1/28 | 5 | NM_213655.5 | A2 | |
WNK1 | ENST00000315939.11 | c.385G>A | p.Ala129Thr | missense_variant | 1/28 | 1 | NM_018979.4 | P2 |
Frequencies
GnomAD3 genomes Cov.: 34
GnomAD3 exomes AF: 0.00000911 AC: 2AN: 219590Hom.: 0 AF XY: 0.0000165 AC XY: 2AN XY: 120976
GnomAD4 exome AF: 0.00000414 AC: 6AN: 1451018Hom.: 0 Cov.: 95 AF XY: 0.00000693 AC XY: 5AN XY: 721284
GnomAD4 genome Cov.: 34
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at