5-81252771-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_001099735.2(CKMT2):c.229C>T(p.Arg77Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000013 in 1,614,228 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 (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R77H) has been classified as Uncertain significance.
Frequency
Consequence
NM_001099735.2 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 rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
CKMT2 | NM_001099735.2 | c.229C>T | p.Arg77Cys | missense_variant | Exon 3 of 10 | ENST00000254035.9 | NP_001093205.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000197 AC: 3AN: 152218Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000119 AC: 3AN: 251450Hom.: 0 AF XY: 0.0000147 AC XY: 2AN XY: 135904
GnomAD4 exome AF: 0.0000123 AC: 18AN: 1461892Hom.: 0 Cov.: 32 AF XY: 0.0000124 AC XY: 9AN XY: 727248
GnomAD4 genome AF: 0.0000197 AC: 3AN: 152336Hom.: 0 Cov.: 32 AF XY: 0.0000268 AC XY: 2AN XY: 74496
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.229C>T (p.R77C) alteration is located in exon 4 (coding exon 2) of the CKMT2 gene. This alteration results from a C to T substitution at nucleotide position 229, causing the arginine (R) at amino acid position 77 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