17-5022380-G-A
Variant summary
Our verdict is Benign. The variant received -13 ACMG points: 0P and 13B. BP4_StrongBP6BS1BS2
The NM_006612.6(KIF1C):c.2299G>A(p.Gly767Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0026 in 1,581,322 control chromosomes in the GnomAD database, including 8 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/22 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. G767E) has been classified as Uncertain significance.
Frequency
Consequence
NM_006612.6 missense
Scores
Clinical Significance
Conservation
Publications
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ACMG classification
Our verdict: Benign. The variant received -13 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
KIF1C | ENST00000320785.10 | c.2299G>A | p.Gly767Arg | missense_variant | Exon 22 of 23 | 1 | NM_006612.6 | ENSP00000320821.5 | ||
KIF1C-AS1 | ENST00000438266.2 | n.172-1425C>T | intron_variant | Intron 1 of 3 | 2 | |||||
KIF1C | ENST00000573815.1 | n.*115G>A | downstream_gene_variant | 5 |
Frequencies
GnomAD3 genomes AF: 0.00154 AC: 235AN: 152274Hom.: 0 Cov.: 32 show subpopulations
GnomAD2 exomes AF: 0.00143 AC: 278AN: 194866 AF XY: 0.00160 show subpopulations
GnomAD4 exome AF: 0.00271 AC: 3879AN: 1428930Hom.: 8 Cov.: 32 AF XY: 0.00266 AC XY: 1882AN XY: 708146 show subpopulations
Age Distribution
GnomAD4 genome AF: 0.00154 AC: 235AN: 152392Hom.: 0 Cov.: 32 AF XY: 0.00148 AC XY: 110AN XY: 74518 show subpopulations
Age Distribution
ClinVar
Submissions by phenotype
Hereditary spastic paraplegia Uncertain:1Benign:1
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not provided Benign:2
KIF1C: BS2 -
See Variant Classification Assertion Criteria. -
KIF1C-related disorder Benign:1
This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -
Spastic ataxia 2 Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at