3-127923936-G-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_207335.4(KBTBD12):c.875G>A(p.Arg292Lys) variant causes a missense change. The variant allele was found at a frequency of 0.0000291 in 1,613,866 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. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Consequence
NM_207335.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
KBTBD12 | NM_207335.4 | c.875G>A | p.Arg292Lys | missense_variant | 2/6 | ENST00000405109.5 | NP_997218.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
KBTBD12 | ENST00000405109.5 | c.875G>A | p.Arg292Lys | missense_variant | 2/6 | 5 | NM_207335.4 | ENSP00000385957.1 |
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152152Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00000803 AC: 2AN: 249026Hom.: 0 AF XY: 0.00000740 AC XY: 1AN XY: 135090
GnomAD4 exome AF: 0.0000315 AC: 46AN: 1461596Hom.: 0 Cov.: 34 AF XY: 0.0000330 AC XY: 24AN XY: 727084
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152270Hom.: 0 Cov.: 32 AF XY: 0.0000134 AC XY: 1AN XY: 74460
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Nov 23, 2024 | The c.875G>A (p.R292K) alteration is located in exon 1 (coding exon 1) of the KBTBD12 gene. This alteration results from a G to A substitution at nucleotide position 875, causing the arginine (R) at amino acid position 292 to be replaced by a lysine (K). 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