17-42780715-C-A
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_032387.5(WNK4):c.17C>A(p.Ala6Asp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000657 in 152,126 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_032387.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
WNK4 | NM_032387.5 | c.17C>A | p.Ala6Asp | missense_variant | 1/19 | ENST00000246914.10 | NP_115763.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
WNK4 | ENST00000246914.10 | c.17C>A | p.Ala6Asp | missense_variant | 1/19 | 1 | NM_032387.5 | ENSP00000246914 | P1 | |
WNK4 | ENST00000591448.5 | c.17C>A | p.Ala6Asp | missense_variant, NMD_transcript_variant | 1/18 | 1 | ENSP00000467088 |
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152126Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00000423 AC: 1AN: 236210Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 130000
GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0AN: 1456452Hom.: 0 Cov.: 31 AF XY: 0.00 AC XY: 0AN XY: 724754
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152126Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74310
ClinVar
Submissions by phenotype
Inborn genetic diseases Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jun 11, 2021 | The c.17C>A (p.A6D) alteration is located in exon 1 (coding exon 1) of the WNK4 gene. This alteration results from a C to A substitution at nucleotide position 17, causing the alanine (A) at amino acid position 6 to be replaced by an aspartic acid (D). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at