13-76885692-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_138444.4(KCTD12):c.457G>A(p.Gly153Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000292 in 1,439,750 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_138444.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
KCTD12 | NM_138444.4 | c.457G>A | p.Gly153Ser | missense_variant | 1/1 | ENST00000377474.4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
KCTD12 | ENST00000377474.4 | c.457G>A | p.Gly153Ser | missense_variant | 1/1 | NM_138444.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000789 AC: 12AN: 152092Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000533 AC: 2AN: 37500Hom.: 0 AF XY: 0.0000475 AC XY: 1AN XY: 21068
GnomAD4 exome AF: 0.0000233 AC: 30AN: 1287658Hom.: 0 Cov.: 31 AF XY: 0.0000317 AC XY: 20AN XY: 631294
GnomAD4 genome ? AF: 0.0000789 AC: 12AN: 152092Hom.: 0 Cov.: 32 AF XY: 0.0000538 AC XY: 4AN XY: 74300
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jan 05, 2022 | The c.457G>A (p.G153S) alteration is located in exon 1 (coding exon 1) of the KCTD12 gene. This alteration results from a G to A substitution at nucleotide position 457, causing the glycine (G) at amino acid position 153 to be replaced by a serine (S). 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