chr17-42787837-G-T
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_032387.5(WNK4):c.1801G>T(p.Ala601Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0211 in 1,612,216 control chromosomes in the GnomAD database, including 2,901 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 Benign (★★).
Frequency
Consequence
NM_032387.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
WNK4 | NM_032387.5 | c.1801G>T | p.Ala601Ser | missense_variant | 8/19 | ENST00000246914.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
WNK4 | ENST00000246914.10 | c.1801G>T | p.Ala601Ser | missense_variant | 8/19 | 1 | NM_032387.5 | P1 | |
WNK4 | ENST00000591448.5 | c.*302G>T | 3_prime_UTR_variant, NMD_transcript_variant | 7/18 | 1 | ||||
WNK4 | ENST00000587705.5 | n.422-293G>T | intron_variant, non_coding_transcript_variant | 4 | |||||
WNK4 | ENST00000592072.1 | n.422-293G>T | intron_variant, non_coding_transcript_variant | 2 |
Frequencies
GnomAD3 genomes AF: 0.0735 AC: 11173AN: 151964Hom.: 1220 Cov.: 32
GnomAD3 exomes AF: 0.0357 AC: 8828AN: 247274Hom.: 682 AF XY: 0.0350 AC XY: 4713AN XY: 134516
GnomAD4 exome AF: 0.0156 AC: 22748AN: 1460134Hom.: 1667 Cov.: 33 AF XY: 0.0174 AC XY: 12635AN XY: 726402
GnomAD4 genome AF: 0.0738 AC: 11231AN: 152082Hom.: 1234 Cov.: 32 AF XY: 0.0734 AC XY: 5458AN XY: 74376
ClinVar
Submissions by phenotype
not provided Benign:2
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 28, 2024 | - - |
Benign, criteria provided, single submitter | clinical testing | GeneDx | May 05, 2021 | This variant is associated with the following publications: (PMID: 19340547) - |
Pseudohypoaldosteronism type 2B Benign:1
Benign, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Mar 06, 2018 | This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at