5-81251166-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 3 ACMG points: 3P and 0B. PM2PP3
The NM_001099735.2(CKMT2):c.34C>T(p.Arg12Cys) variant causes a missense change. The variant allele was found at a frequency of 0.00000867 in 1,613,910 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R12H) has been classified as Uncertain significance.
Frequency
Consequence
NM_001099735.2 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Uncertain_significance. Variant got 3 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
CKMT2 | NM_001099735.2 | c.34C>T | p.Arg12Cys | missense_variant | Exon 2 of 10 | ENST00000254035.9 | NP_001093205.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152134Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000159 AC: 4AN: 251352Hom.: 0 AF XY: 0.0000221 AC XY: 3AN XY: 135838
GnomAD4 exome AF: 0.00000889 AC: 13AN: 1461776Hom.: 0 Cov.: 31 AF XY: 0.00000825 AC XY: 6AN XY: 727206
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152134Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74296
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.34C>T (p.R12C) alteration is located in exon 3 (coding exon 1) of the CKMT2 gene. This alteration results from a C to T substitution at nucleotide position 34, causing the arginine (R) at amino acid position 12 to be replaced by a cysteine (C). 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