rs747424547
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 3P and 2B. PM2PP3BP6_Moderate
The NM_006612.6(KIF1C):c.14C>T(p.Ser5Leu) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0000572 in 1,573,766 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Likely benign (★). Synonymous variant affecting the same amino acid position (i.e. S5S) has been classified as Benign.
Frequency
Consequence
NM_006612.6 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
KIF1C | NM_006612.6 | c.14C>T | p.Ser5Leu | missense_variant | 3/23 | ENST00000320785.10 | |
KIF1C | XM_005256424.3 | c.14C>T | p.Ser5Leu | missense_variant | 4/24 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
KIF1C | ENST00000320785.10 | c.14C>T | p.Ser5Leu | missense_variant | 3/23 | 1 | NM_006612.6 | P1 | |
KIF1C | ENST00000574165.1 | c.14C>T | p.Ser5Leu | missense_variant | 4/7 | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.0000394 AC: 6AN: 152160Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000953 AC: 18AN: 188804Hom.: 0 AF XY: 0.000109 AC XY: 11AN XY: 101306
GnomAD4 exome AF: 0.0000591 AC: 84AN: 1421606Hom.: 0 Cov.: 30 AF XY: 0.0000597 AC XY: 42AN XY: 703734
GnomAD4 genome ? AF: 0.0000394 AC: 6AN: 152160Hom.: 0 Cov.: 33 AF XY: 0.0000673 AC XY: 5AN XY: 74326
ClinVar
Submissions by phenotype
Spastic ataxia 2 Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Aug 10, 2022 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at