17-21415386-C-T
Variant summary
Our verdict is Likely benign. Variant got -3 ACMG points: 3P and 6B. PM2PP2BP4_StrongBP6_Moderate
The NM_021012.5(KCNJ12):c.44C>T(p.Ser15Leu) variant causes a missense change. The variant allele was found at a frequency of 0.0000657 in 152,286 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 Benign (★). Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.
Frequency
Consequence
NM_021012.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -3 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
KCNJ12 | NM_021012.5 | c.44C>T | p.Ser15Leu | missense_variant | 3/3 | ENST00000583088.6 | |
KCNJ12 | XM_005256625.6 | c.44C>T | p.Ser15Leu | missense_variant | 3/3 | ||
KCNJ12 | XM_011523831.3 | c.44C>T | p.Ser15Leu | missense_variant | 3/3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
KCNJ12 | ENST00000583088.6 | c.44C>T | p.Ser15Leu | missense_variant | 3/3 | 1 | NM_021012.5 | P1 | |
KCNJ12 | ENST00000331718.5 | c.44C>T | p.Ser15Leu | missense_variant | 3/3 | 1 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000657 AC: 10AN: 152286Hom.: 0 Cov.: 68
GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.0000281 AC: 41AN: 1460068Hom.: 0 Cov.: 209 AF XY: 0.0000330 AC XY: 24AN XY: 726420
GnomAD4 genome AF: 0.0000657 AC: 10AN: 152286Hom.: 0 Cov.: 68 AF XY: 0.0000538 AC XY: 4AN XY: 74406
ClinVar
Submissions by phenotype
KCNJ12-related disorder Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Oct 17, 2019 | This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at