15-69417422-G-A
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BS2
The NM_001367805.3(KIF23):c.121G>A(p.Glu41Lys) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0000089 in 1,460,852 control chromosomes in the GnomAD database, with no homozygous occurrence. 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 -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
KIF23 | NM_001367805.3 | c.121G>A | p.Glu41Lys | 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.121G>A | p.Glu41Lys | missense_variant | Exon 3 of 24 | NM_001367805.3 | ENSP00000504770.1 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 exomes AF: 0.00000399 AC: 1AN: 250490Hom.: 0 AF XY: 0.00000738 AC XY: 1AN XY: 135452
GnomAD4 exome AF: 0.00000890 AC: 13AN: 1460852Hom.: 0 Cov.: 32 AF XY: 0.00000688 AC XY: 5AN XY: 726744
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.121G>A (p.E41K) alteration is located in exon 3 (coding exon 3) of the KIF23 gene. This alteration results from a G to A substitution at nucleotide position 121, causing the glutamic acid (E) at amino acid position 41 to be replaced by a lysine (K). 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