17-21415349-G-A
Variant summary
Our verdict is Likely benign. Variant got -1 ACMG points: 3P and 4B. PM2PP2BP4_Strong
The NM_021012.5(KCNJ12):c.7G>A(p.Ala3Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000311 in 1,607,222 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 (★). Synonymous variant affecting the same amino acid position (i.e. A3A) has been classified as Benign.
Frequency
Consequence
NM_021012.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
KCNJ12 | NM_021012.5 | c.7G>A | p.Ala3Thr | missense_variant | 3/3 | ENST00000583088.6 | |
KCNJ12 | XM_005256625.6 | c.7G>A | p.Ala3Thr | missense_variant | 3/3 | ||
KCNJ12 | XM_011523831.3 | c.7G>A | p.Ala3Thr | missense_variant | 3/3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
KCNJ12 | ENST00000583088.6 | c.7G>A | p.Ala3Thr | missense_variant | 3/3 | 1 | NM_021012.5 | P1 | |
KCNJ12 | ENST00000331718.5 | c.7G>A | p.Ala3Thr | missense_variant | 3/3 | 1 | P1 |
Frequencies
GnomAD3 genomes AF: 0.000105 AC: 16AN: 152294Hom.: 0 Cov.: 64
GnomAD3 exomes AF: 0.0000201 AC: 5AN: 248538Hom.: 0 AF XY: 0.0000148 AC XY: 2AN XY: 134794
GnomAD4 exome AF: 0.0000234 AC: 34AN: 1454810Hom.: 0 Cov.: 122 AF XY: 0.0000207 AC XY: 15AN XY: 724050
GnomAD4 genome AF: 0.000105 AC: 16AN: 152412Hom.: 0 Cov.: 64 AF XY: 0.0000402 AC XY: 3AN XY: 74536
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Mar 01, 2024 | The c.7G>A (p.A3T) alteration is located in exon 3 (coding exon 1) of the KCNJ12 gene. This alteration results from a G to A substitution at nucleotide position 7, causing the alanine (A) at amino acid position 3 to be replaced by a threonine (T). 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