17-5002851-GCCCC-GCCCCC

Variant names:

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

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+20dupC 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 0.0083 (16 hom., cov: 0)
  • Exomes 𝑓: 0.031 (6 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-G-GC is Benign according to our data. Variant chr17-5002851-G-GC is described in ClinVar as [Likely_benign]. Clinvar id is 468859.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• BA1: GnomAdExome4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.0858 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
KIF1C	NM_006612.6	c.720+20dupC		intron_variant	Intron 8 of 22	ENST00000320785.10	NP_006603.2
KIF1C	XM_005256424.3	c.720+20dupC		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+9_720+10insC		intron_variant	Intron 8 of 22	1	NM_006612.6	ENSP00000320821.5

Frequencies

GnomAD3 genomes AF: 0.00831 AC: 1138 AN: 136932 Hom.: 16 Cov.: 0

Gnomad AFR AF: 0.00257

Gnomad AMI AF: 0.00346

Gnomad AMR AF: 0.00846

Gnomad ASJ AF: 0.0257

Gnomad EAS AF: 0.0115

Gnomad SAS AF: 0.0236

Gnomad FIN AF: 0.00412

Gnomad MID AF: 0.0132

Gnomad NFE AF: 0.00984

Gnomad OTH AF: 0.0136

GnomAD4 exome AF: 0.0312 AC: 39279 AN: 1257914 Hom.: 6 Cov.: 0 AF XY: 0.0331 AC XY: 20787 AN XY: 628022

Gnomad4 AFR exome AF: 0.00749

Gnomad4 AMR exome AF: 0.0338

Gnomad4 ASJ exome AF: 0.0422

Gnomad4 EAS exome AF: 0.0368

Gnomad4 SAS exome AF: 0.0876

Gnomad4 FIN exome AF: 0.0149

Gnomad4 NFE exome AF: 0.0278

Gnomad4 OTH exome AF: 0.0310

GnomAD4 genome AF: 0.00831 AC: 1139 AN: 137006 Hom.: 16 Cov.: 0 AF XY: 0.00835 AC XY: 550 AN XY: 65844

Gnomad4 AFR AF: 0.00262

Gnomad4 AMR AF: 0.00845

Gnomad4 ASJ AF: 0.0257

Gnomad4 EAS AF: 0.0113

Gnomad4 SAS AF: 0.0238

Gnomad4 FIN AF: 0.00412

Gnomad4 NFE AF: 0.00984

Gnomad4 OTH AF: 0.0134

ClinVar

Significance: Benign/Likely benign

Submissions summary: Benign:3

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

Spastic ataxia 2 Benign:1

Jan 29, 2025

Labcorp Genetics (formerly Invitae), Labcorp

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Hereditary spastic paraplegia Benign:1

Jan 21, 2022

Genome Diagnostics Laboratory, The Hospital for Sick Children

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

not provided Benign:1

Sep 12, 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;