9-114091916-TG-T
Variant summary
Our verdict is Uncertain significance. Variant got 3 ACMG points: 4P and 1B. PVS1_ModeratePM2BS1_Supporting
The NM_001388308.1(KIF12):c.1900delC(p.Gln634SerfsTer30) variant causes a frameshift change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000088 in 1,612,966 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001388308.1 frameshift
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 rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
KIF12 | NM_001388308.1 | c.1900delC | p.Gln634SerfsTer30 | frameshift_variant | Exon 19 of 19 | ENST00000640217.2 | NP_001375237.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
KIF12 | ENST00000640217.2 | c.1900delC | p.Gln634SerfsTer30 | frameshift_variant | Exon 19 of 19 | 5 | NM_001388308.1 | ENSP00000491702.1 |
Frequencies
GnomAD3 genomes AF: 0.0000394 AC: 6AN: 152216Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000890 AC: 22AN: 247284Hom.: 0 AF XY: 0.0000670 AC XY: 9AN XY: 134398
GnomAD4 exome AF: 0.0000931 AC: 136AN: 1460632Hom.: 0 Cov.: 31 AF XY: 0.0000867 AC XY: 63AN XY: 726582
GnomAD4 genome AF: 0.0000394 AC: 6AN: 152334Hom.: 0 Cov.: 32 AF XY: 0.0000537 AC XY: 4AN XY: 74496
ClinVar
Submissions by phenotype
not provided Uncertain:1
This sequence change results in a frameshift in the KIF12 gene (p.Gln496Serfs*30). While this is not anticipated to result in nonsense mediated decay, it is expected to disrupt the last 18 amino acid(s) of the KIF12 protein and extend the protein by 11 additional amino acid residues. This variant is present in population databases (rs776506245, gnomAD 0.09%). This variant has not been reported in the literature in individuals affected with KIF12-related conditions. Experimental studies and prediction algorithms are not available or were not evaluated, and the functional significance of this variant is currently unknown. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at