15-69416058-G-A
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2
The NM_001367805.3(KIF23):c.76G>A(p.Val26Ile) variant causes a missense change. The variant allele was found at a frequency of 0.000255 in 1,572,286 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001367805.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
KIF23 | NM_001367805.3 | c.76G>A | p.Val26Ile | missense_variant | Exon 2 of 24 | ENST00000679126.1 | NP_001354734.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
KIF23 | ENST00000679126.1 | c.76G>A | p.Val26Ile | missense_variant | Exon 2 of 24 | NM_001367805.3 | ENSP00000504770.1 |
Frequencies
GnomAD3 genomes AF: 0.000177 AC: 27AN: 152226Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000139 AC: 30AN: 215310Hom.: 0 AF XY: 0.000136 AC XY: 16AN XY: 117848
GnomAD4 exome AF: 0.000263 AC: 374AN: 1419942Hom.: 0 Cov.: 28 AF XY: 0.000238 AC XY: 168AN XY: 705996
GnomAD4 genome AF: 0.000177 AC: 27AN: 152344Hom.: 0 Cov.: 33 AF XY: 0.000188 AC XY: 14AN XY: 74504
ClinVar
Submissions by phenotype
not provided Uncertain:1
This sequence change replaces valine, which is neutral and non-polar, with isoleucine, which is neutral and non-polar, at codon 26 of the KIF23 protein (p.Val26Ile). This variant is present in population databases (rs139012996, gnomAD 0.02%). This variant has not been reported in the literature in individuals affected with KIF23-related conditions. ClinVar contains an entry for this variant (Variation ID: 2175905). Invitae Evidence Modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) indicates that this missense variant is not expected to disrupt KIF23 protein function with a negative predictive value of 80%. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at