NM_006648.4:c.2060C>T
Variant summary
Our verdict is Likely benign. The variant received -6 ACMG points: 0P and 6B. BP4_ModerateBS2
The NM_006648.4(WNK2):c.2060C>T(p.Pro687Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0004 in 1,579,926 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. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_006648.4 missense
Scores
Clinical Significance
Conservation
Publications
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ACMG classification
Our verdict: Likely_benign. The variant received -6 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.000151 AC: 23AN: 152202Hom.: 0 Cov.: 33 show subpopulations
GnomAD2 exomes AF: 0.000141 AC: 28AN: 198276 AF XY: 0.000164 show subpopulations
GnomAD4 exome AF: 0.000427 AC: 609AN: 1427724Hom.: 0 Cov.: 31 AF XY: 0.000394 AC XY: 279AN XY: 708582 show subpopulations
Age Distribution
GnomAD4 genome AF: 0.000151 AC: 23AN: 152202Hom.: 0 Cov.: 33 AF XY: 0.0000941 AC XY: 7AN XY: 74350 show subpopulations
Age Distribution
ClinVar
Submissions by phenotype
not specified Uncertain:1
The p.P687L variant (also known as c.2060C>T), located in coding exon 9 of the WNK2 gene, results from a C to T substitution at nucleotide position 2060. The proline at codon 687 is replaced by leucine, an amino acid with similar properties. This amino acid position is conserved. In addition, this alteration is predicted to be tolerated by in silico analysis. Based on the available evidence, the clinical significance of this variant remains unclear. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at