chr15-69417401-C-A
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 0P and 5B. BP6BS2
The NM_001367805.3(KIF23):c.100C>A(p.Pro34Thr) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.000721 in 1,610,982 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Consequence
NM_001367805.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -5 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
KIF23 | NM_001367805.3 | c.100C>A | p.Pro34Thr | missense_variant | Exon 3 of 24 | ENST00000679126.1 | NP_001354734.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
KIF23 | ENST00000679126.1 | c.100C>A | p.Pro34Thr | missense_variant | Exon 3 of 24 | NM_001367805.3 | ENSP00000504770.1 |
Frequencies
GnomAD3 genomes AF: 0.000572 AC: 87AN: 152142Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000579 AC: 144AN: 248588Hom.: 0 AF XY: 0.000580 AC XY: 78AN XY: 134468
GnomAD4 exome AF: 0.000736 AC: 1074AN: 1458722Hom.: 0 Cov.: 32 AF XY: 0.000736 AC XY: 534AN XY: 725698
GnomAD4 genome AF: 0.000571 AC: 87AN: 152260Hom.: 0 Cov.: 33 AF XY: 0.000537 AC XY: 40AN XY: 74448
ClinVar
Submissions by phenotype
not provided Uncertain:1Benign:1
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not specified Uncertain:1
The c.100C>A (p.P34T) alteration is located in exon 3 (coding exon 3) of the KIF23 gene. This alteration results from a C to A substitution at nucleotide position 100, causing the proline (P) at amino acid position 34 to be replaced by a threonine (T). 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