17-5002851-GCCCC-GCCC

Variant names:

• chr17-5002851-GC-G
• rs10533622
• NM_006612.6:c.720+20delC

Variant summary

Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP6_Very_Strong BA1

The NM_006612.6(KIF1C):​c.720+20delC variant causes a intron change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Likely benign (★★).

• Frequency:
  • Genomes: 𝑓 0.038 (87 hom., cov: 0)
  • Exomes 𝑓: 0.12 (1071 hom.)
• Consequence: KIF1C NM_006612.6 intron
• Clinical Significance: Benign/Likely benign criteria provided, multiple submitters, no conflicts B:3
• 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]

ACMG classification

Verdict is Benign. Variant got -16 ACMG points.

• BP6: Variant 17-5002851-GC-G is Benign according to our data. Variant chr17-5002851-GC-G is described in ClinVar as [Likely_benign]. Clinvar id is 1167058.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0533 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
KIF1C	NM_006612.6	c.720+20delC		intron_variant	Intron 8 of 22	ENST00000320785.10	NP_006603.2
KIF1C	XM_005256424.3	c.720+20delC		intron_variant	Intron 9 of 23		XP_005256481.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
KIF1C	ENST00000320785.10	c.720+10delC		intron_variant	Intron 8 of 22	1	NM_006612.6	ENSP00000320821.5

Frequencies

GnomAD3 genomes AF: 0.0383 AC: 5240 AN: 136808 Hom.: 87 Cov.: 0

Gnomad AFR AF: 0.0186

Gnomad AMI AF: 0.0876

Gnomad AMR AF: 0.0375

Gnomad ASJ AF: 0.0327

Gnomad EAS AF: 0.00198

Gnomad SAS AF: 0.00901

Gnomad FIN AF: 0.0294

Gnomad MID AF: 0.0563

Gnomad NFE AF: 0.0548

Gnomad OTH AF: 0.0353

GnomAD4 exome AF: 0.115 AC: 137136 AN: 1188546 Hom.: 1071 Cov.: 0 AF XY: 0.118 AC XY: 69589 AN XY: 591930

Gnomad4 AFR exome AF: 0.0417

Gnomad4 AMR exome AF: 0.150

Gnomad4 ASJ exome AF: 0.122

Gnomad4 EAS exome AF: 0.0907

Gnomad4 SAS exome AF: 0.108

Gnomad4 FIN exome AF: 0.112

Gnomad4 NFE exome AF: 0.118

Gnomad4 OTH exome AF: 0.111

GnomAD4 genome AF: 0.0383 AC: 5236 AN: 136878 Hom.: 87 Cov.: 0 AF XY: 0.0358 AC XY: 2357 AN XY: 65786

Gnomad4 AFR AF: 0.0186

Gnomad4 AMR AF: 0.0374

Gnomad4 ASJ AF: 0.0327

Gnomad4 EAS AF: 0.00199

Gnomad4 SAS AF: 0.00906

Gnomad4 FIN AF: 0.0294

Gnomad4 NFE AF: 0.0548

Gnomad4 OTH AF: 0.0350

ClinVar

Significance: Benign/Likely benign

Submissions summary: Benign:3

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

Spastic ataxia 2 Benign:1

Feb 03, 2025

Labcorp Genetics (formerly Invitae), Labcorp

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Hereditary spastic paraplegia Benign:1

Dec 12, 2016

Genome Diagnostics Laboratory, The Hospital for Sick Children

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

not provided Benign:1

Aug 06, 2019

GeneDx

Significance: Likely benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.020		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs10533622; hg19: chr17-4906146;