15-69417385-A-G
Variant summary
Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_StrongBP6_ModerateBP7BS2
The NM_001367805.3(KIF23):āc.84A>Gā(p.Val28Val) variant causes a splice region, synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000388 in 1,598,048 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. 1/1 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Benign (ā ).
Frequency
Consequence
NM_001367805.3 splice_region, synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -11 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
KIF23 | NM_001367805.3 | c.84A>G | p.Val28Val | splice_region_variant, synonymous_variant | 3/24 | ENST00000679126.1 | NP_001354734.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
KIF23 | ENST00000679126.1 | c.84A>G | p.Val28Val | splice_region_variant, synonymous_variant | 3/24 | NM_001367805.3 | ENSP00000504770.1 |
Frequencies
GnomAD3 genomes AF: 0.000217 AC: 33AN: 152234Hom.: 1 Cov.: 32
GnomAD3 exomes AF: 0.000109 AC: 26AN: 238242Hom.: 0 AF XY: 0.0000544 AC XY: 7AN XY: 128650
GnomAD4 exome AF: 0.0000187 AC: 27AN: 1445696Hom.: 0 Cov.: 32 AF XY: 0.00000835 AC XY: 6AN XY: 718744
GnomAD4 genome AF: 0.000230 AC: 35AN: 152352Hom.: 1 Cov.: 32 AF XY: 0.000188 AC XY: 14AN XY: 74512
ClinVar
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Nov 07, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at