rs146679209
Variant summary
Our verdict is Benign. Variant got -11 ACMG points: 2P and 13B. PM2BP4_StrongBP6_Very_StrongBP7
The NM_006612.6(KIF1C):c.2481G>A(p.Gly827=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000475 in 1,594,470 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Genomes: 𝑓 0.00022 ( 0 hom., cov: 32)
Exomes 𝑓: 0.00050 ( 0 hom. )
Consequence
KIF1C
NM_006612.6 synonymous
NM_006612.6 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.410
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 Benign. Variant got -11 ACMG points.
PM2
?
Very rare variant in population databases, with high coverage;
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.51).
BP6
?
Variant 17-5022562-G-A is Benign according to our data. Variant chr17-5022562-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 468852.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr17-5022562-G-A is described in Lovd as [Likely_benign].
BP7
?
Synonymous conserved (PhyloP=-0.41 with no splicing effect.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
KIF1C | NM_006612.6 | c.2481G>A | p.Gly827= | synonymous_variant | 22/23 | ENST00000320785.10 | |
KIF1C | XM_005256424.3 | c.2481G>A | p.Gly827= | synonymous_variant | 23/24 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
KIF1C | ENST00000320785.10 | c.2481G>A | p.Gly827= | synonymous_variant | 22/23 | 1 | NM_006612.6 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.000217 AC: 33AN: 152236Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.000233 AC: 50AN: 215004Hom.: 0 AF XY: 0.000216 AC XY: 25AN XY: 115804
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GnomAD4 exome AF: 0.000503 AC: 725AN: 1442234Hom.: 0 Cov.: 32 AF XY: 0.000489 AC XY: 350AN XY: 715572
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GnomAD4 genome ? AF: 0.000217 AC: 33AN: 152236Hom.: 0 Cov.: 32 AF XY: 0.000148 AC XY: 11AN XY: 74374
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ClinVar
Significance: Likely benign
Submissions summary: Benign:3
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Jul 24, 2017 | This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. - |
Spastic ataxia 2 Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Aug 10, 2023 | - - |
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Feb 01, 2024 | KIF1C: BP4, BP7 - |
Computational scores
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BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at