chr17-5002851-GCCC-G
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP6_Very_StrongBS2
The NM_006612.6(KIF1C):c.720+18_720+20del variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000216 in 1,421,838 control chromosomes in the GnomAD database, including 2 homozygotes. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Genomes: 𝑓 0.00039 ( 0 hom., cov: 0)
Exomes 𝑓: 0.00020 ( 2 hom. )
Consequence
KIF1C
NM_006612.6 intron
NM_006612.6 intron
Scores
Not classified
Clinical Significance
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 Benign. Variant got -12 ACMG points.
BP6
Variant 17-5002851-GCCC-G is Benign according to our data. Variant chr17-5002851-GCCC-G is described in ClinVar as [Likely_benign]. Clinvar id is 1344413.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BS2
High Homozygotes in GnomAdExome4 at 2 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
KIF1C | NM_006612.6 | c.720+18_720+20del | intron_variant | ENST00000320785.10 | |||
KIF1C | XM_005256424.3 | c.720+18_720+20del | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
KIF1C | ENST00000320785.10 | c.720+18_720+20del | intron_variant | 1 | NM_006612.6 | P1 |
Frequencies
GnomAD3 genomes AF: 0.000394 AC: 54AN: 137022Hom.: 0 Cov.: 0
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GnomAD4 exome AF: 0.000197 AC: 253AN: 1284742Hom.: 2 AF XY: 0.000195 AC XY: 125AN XY: 642126
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GnomAD4 genome AF: 0.000394 AC: 54AN: 137096Hom.: 0 Cov.: 0 AF XY: 0.000425 AC XY: 28AN XY: 65898
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ClinVar
Significance: Benign/Likely benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
Spastic ataxia 2 Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Dec 11, 2023 | - - |
Hereditary spastic paraplegia Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Genome Diagnostics Laboratory, The Hospital for Sick Children | Apr 26, 2021 | - - |
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at