9-114093229-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 3 ACMG points: 3P and 0B. PM2PP3
The NM_001388308.1(KIF12):c.1596G>A(p.Gln532=) variant causes a splice region, synonymous change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predicting alterations to normal splicing. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001388308.1 splice_region, synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 3 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
KIF12 | NM_001388308.1 | c.1596G>A | p.Gln532= | splice_region_variant, synonymous_variant | 16/19 | ENST00000640217.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
KIF12 | ENST00000640217.2 | c.1596G>A | p.Gln532= | splice_region_variant, synonymous_variant | 16/19 | 5 | NM_001388308.1 | P1 | |
KIF12 | ENST00000640553.1 | n.1420G>A | splice_region_variant, non_coding_transcript_exon_variant | 13/16 | 1 | ||||
KIF12 | ENST00000498016.1 | c.301G>A | p.Asp101Asn | missense_variant, splice_region_variant | 2/3 | 5 | |||
KIF12 | ENST00000639832.1 | n.1827G>A | splice_region_variant, non_coding_transcript_exon_variant | 14/18 | 2 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD4 exome Cov.: 33
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
not provided Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | GeneDx | Aug 30, 2022 | Not observed at significant frequency in large population cohorts (gnomAD); In silico analysis supports a deleterious effect on splicing; Has not been previously published as pathogenic or benign to our knowledge - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
No publications associated with this variant yet.