rs144431404
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_018204.5(CKAP2):āc.778C>Gā(p.His260Asp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000657 in 152,174 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. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. H260L) has been classified as Uncertain significance.
Frequency
Consequence
NM_018204.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CKAP2 | ENST00000258607.10 | c.778C>G | p.His260Asp | missense_variant | Exon 4 of 9 | 1 | NM_018204.5 | ENSP00000258607.5 | ||
CKAP2 | ENST00000378037.9 | c.781C>G | p.His261Asp | missense_variant | Exon 4 of 9 | 1 | ENSP00000367276.4 | |||
CKAP2 | ENST00000378034.7 | c.778C>G | p.His260Asp | missense_variant | Exon 4 of 6 | 1 | ENSP00000367273.2 | |||
CKAP2 | ENST00000490903.5 | c.634C>G | p.His212Asp | missense_variant | Exon 4 of 9 | 2 | ENSP00000417830.1 |
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152174Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.00000398 AC: 1AN: 251380Hom.: 0 AF XY: 0.00000736 AC XY: 1AN XY: 135858
GnomAD4 exome Cov.: 32
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152174Hom.: 0 Cov.: 31 AF XY: 0.0000135 AC XY: 1AN XY: 74330
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at