5-81255186-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 3 ACMG points: 3P and 0B. PM2PP3
The NM_001099735.2(CKMT2):c.641C>T(p.Thr214Met) variant causes a missense change. The variant allele was found at a frequency of 0.0000372 in 1,614,038 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 (★).
Frequency
Consequence
NM_001099735.2 missense
Scores
Clinical Significance
Conservation
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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.641C>T | p.Thr214Met | missense_variant | Exon 5 of 10 | ENST00000254035.9 | NP_001093205.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000460 AC: 7AN: 152180Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000200 AC: 5AN: 250470Hom.: 0 AF XY: 0.0000221 AC XY: 3AN XY: 135572
GnomAD4 exome AF: 0.0000363 AC: 53AN: 1461740Hom.: 0 Cov.: 31 AF XY: 0.0000385 AC XY: 28AN XY: 727170
GnomAD4 genome AF: 0.0000460 AC: 7AN: 152298Hom.: 0 Cov.: 32 AF XY: 0.0000403 AC XY: 3AN XY: 74476
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.641C>T (p.T214M) alteration is located in exon 6 (coding exon 4) of the CKMT2 gene. This alteration results from a C to T substitution at nucleotide position 641, causing the threonine (T) at amino acid position 214 to be replaced by a methionine (M). 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