17-5002851-GCCCC-GCC

Variant names:

• chr17-5002851-GCC-G
• rs10533622
• NM_006612.6:c.720+19_720+20delCC

Variant summary

Our verdict is Benign. The variant received -16 ACMG points: 0P and 16B. BP6_Very_Strong BA1

The NM_006612.6(KIF1C):​c.720+19_720+20delCC variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.304 in 1,420,046 control chromosomes in the GnomAD database, including 64,151 homozygotes. Variant has been reported in ClinVar as Benign (★★).

• Frequency:
  • Genomes: 𝑓 0.36 (10190 hom., cov: 0)
  • Exomes 𝑓: 0.30 (53961 hom.)
• Consequence: KIF1C NM_006612.6 intron
• Clinical Significance: Benign criteria provided, multiple submitters, no conflicts B:3
• Conservation: PhyloP100: 2.04
• Publications: 1 publications found

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]

KIF1C Gene-Disease associations (from GenCC):

• spastic ataxia 2

  Inheritance: AR, AD Classification: STRONG, MODERATE, SUPPORTIVE Submitted by: Labcorp Genetics (formerly Invitae), Ambry Genetics, Orphanet

ACMG classification

Our verdict: Benign. The variant received -16 ACMG points.

• BP6: Variant 17-5002851-GCC-G is Benign according to our data. Variant chr17-5002851-GCC-G is described in ClinVar as Benign. ClinVar VariationId is 516675.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.584 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_006612.6. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	KIF1C	NM_006612.6	MANE Select	c.720+19_720+20delCC		intron	N/A	NP_006603.2

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	KIF1C	ENST00000320785.10	TSL:1 MANE Select	c.720+10_720+11delCC		intron	N/A	ENSP00000320821.5

Frequencies

GnomAD3 genomes AF: 0.364 AC: 49848 AN: 137048 Hom.: 10183 Cov.: 0

Gnomad AFR AF: 0.591

Gnomad AMI AF: 0.159

Gnomad AMR AF: 0.297

Gnomad ASJ AF: 0.274

Gnomad EAS AF: 0.283

Gnomad SAS AF: 0.208

Gnomad FIN AF: 0.353

Gnomad MID AF: 0.430

Gnomad NFE AF: 0.274

Gnomad OTH AF: 0.364

GnomAD2 exomes AF: 0.352 AC: 68026 AN: 193244 AF XY: 0.342

Gnomad AFR exome AF: 0.643

Gnomad AMR exome AF: 0.320

Gnomad ASJ exome AF: 0.339

Gnomad EAS exome AF: 0.350

Gnomad FIN exome AF: 0.424

Gnomad NFE exome AF: 0.326

Gnomad OTH exome AF: 0.378

GnomAD4 exome AF: 0.297 AC: 381157 AN: 1282924 Hom.: 53961 AF XY: 0.294 AC XY: 188397 AN XY: 641236

African (AFR) AF: 0.619 AC: 19278 AN: 31140

American (AMR) AF: 0.269 AC: 10957 AN: 40666

Ashkenazi Jewish (ASJ) AF: 0.289 AC: 6759 AN: 23406

East Asian (EAS) AF: 0.338 AC: 12305 AN: 36352

South Asian (SAS) AF: 0.211 AC: 16390 AN: 77626

European-Finnish (FIN) AF: 0.372 AC: 17202 AN: 46224

Middle Eastern (MID) AF: 0.413 AC: 1653 AN: 4004

European-Non Finnish (NFE) AF: 0.288 AC: 279611 AN: 969946

Other (OTH) AF: 0.317 AC: 17002 AN: 53560

GnomAD4 genome AF: 0.364 AC: 49886 AN: 137122 Hom.: 10190 Cov.: 0 AF XY: 0.366 AC XY: 24091 AN XY: 65910

African (AFR) AF: 0.591 AC: 21415 AN: 36248

American (AMR) AF: 0.297 AC: 4020 AN: 13522

Ashkenazi Jewish (ASJ) AF: 0.274 AC: 909 AN: 3312

East Asian (EAS) AF: 0.283 AC: 1281 AN: 4522

South Asian (SAS) AF: 0.206 AC: 842 AN: 4086

European-Finnish (FIN) AF: 0.353 AC: 2917 AN: 8252

Middle Eastern (MID) AF: 0.429 AC: 121 AN: 282

European-Non Finnish (NFE) AF: 0.274 AC: 17570 AN: 64162

Other (OTH) AF: 0.360 AC: 673 AN: 1868

Alfa AF: 0.212 Hom.: 580

ClinVar

Significance: Benign

Submissions summary: Benign:3

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

not provided Benign:2

May 29, 2018

GeneDx

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

Mar 08, 2016

GeneDx

Significance: Benign

Review Status: flagged submission

Collection Method: clinical testing

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

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		2.0
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.050		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs10533622; hg19: chr17-4906146;