chr12-861273-A-G
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 2P and 7B. PM2BP4_StrongBP6_ModerateBP7
The NM_213655.5(WNK1):āc.1881A>Gā(p.Val627=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000274 in 1,461,870 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (ā ). Synonymous variant affecting the same amino acid position (i.e. V627V) has been classified as Likely benign.
Frequency
Consequence
NM_213655.5 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -5 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
WNK1 | NM_213655.5 | c.1881A>G | p.Val627= | synonymous_variant | 7/28 | ENST00000340908.9 | |
WNK1 | NM_018979.4 | c.1881A>G | p.Val627= | synonymous_variant | 7/28 | ENST00000315939.11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
WNK1 | ENST00000340908.9 | c.1881A>G | p.Val627= | synonymous_variant | 7/28 | 5 | NM_213655.5 | A2 | |
WNK1 | ENST00000315939.11 | c.1881A>G | p.Val627= | synonymous_variant | 7/28 | 1 | NM_018979.4 | P2 |
Frequencies
GnomAD3 genomes Cov.: 31
GnomAD3 exomes AF: 0.0000159 AC: 4AN: 250794Hom.: 0 AF XY: 0.0000221 AC XY: 3AN XY: 135536
GnomAD4 exome AF: 0.00000274 AC: 4AN: 1461870Hom.: 0 Cov.: 33 AF XY: 0.00000413 AC XY: 3AN XY: 727234
GnomAD4 genome Cov.: 31
ClinVar
Submissions by phenotype
Pseudohypoaldosteronism type 2C;C2752089:Neuropathy, hereditary sensory and autonomic, type 2A Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Nov 12, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at