rs10533622
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_006612.6(KIF1C):c.720+17_720+20del variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000352 in 1,422,118 control chromosomes in the GnomAD database, with no homozygous occurrence. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.000022 ( 0 hom., cov: 0)
Exomes 𝑓: 0.0000016 ( 0 hom. )
Consequence
KIF1C
NM_006612.6 intron
NM_006612.6 intron
Scores
Not classified
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 2.04
Genes affected
KIF1C (HGNC:6317): (kinesin family member 1C) The protein encoded by this gene is a member of the kinesin-like protein family. The family members are microtubule-dependent molecular motors that transport organelles within cells and move chromosomes during cell division. Mutations in this gene are a cause of spastic ataxia 2, autosomal recessive. [provided by RefSeq, May 2014]
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ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 2 ACMG points.
PM2
?
Very rare variant in population databases, with high coverage;
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
KIF1C | NM_006612.6 | c.720+17_720+20del | intron_variant | ENST00000320785.10 | |||
KIF1C | XM_005256424.3 | c.720+17_720+20del | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
KIF1C | ENST00000320785.10 | c.720+17_720+20del | intron_variant | 1 | NM_006612.6 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000219 AC: 3AN: 137024Hom.: 0 Cov.: 0
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GnomAD4 exome AF: 0.00000156 AC: 2AN: 1285094Hom.: 0 AF XY: 0.00000156 AC XY: 1AN XY: 642278
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GnomAD4 genome ? AF: 0.0000219 AC: 3AN: 137024Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0AN XY: 65826
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ClinVar
Not reported inComputational scores
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at