15-69416069-G-A
Variant summary
Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP4_StrongBP6_Very_StrongBS2
The NM_001367805.3(KIF23):c.81+6G>A variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00073 in 1,555,652 control chromosomes in the GnomAD database, including 6 homozygotes. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Benign (★★).
Frequency
Consequence
NM_001367805.3 splice_region, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -16 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
KIF23 | NM_001367805.3 | c.81+6G>A | splice_region_variant, intron_variant | Intron 2 of 23 | ENST00000679126.1 | NP_001354734.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
KIF23 | ENST00000679126.1 | c.81+6G>A | splice_region_variant, intron_variant | Intron 2 of 23 | NM_001367805.3 | ENSP00000504770.1 |
Frequencies
GnomAD3 genomes AF: 0.00394 AC: 600AN: 152182Hom.: 1 Cov.: 33
GnomAD3 exomes AF: 0.00108 AC: 223AN: 206100Hom.: 1 AF XY: 0.000743 AC XY: 84AN XY: 113036
GnomAD4 exome AF: 0.000383 AC: 537AN: 1403352Hom.: 5 Cov.: 27 AF XY: 0.000341 AC XY: 238AN XY: 697738
GnomAD4 genome AF: 0.00393 AC: 599AN: 152300Hom.: 1 Cov.: 33 AF XY: 0.00375 AC XY: 279AN XY: 74474
ClinVar
Submissions by phenotype
not provided Benign:2
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KIF23-related disorder Benign:1
This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at