Genetic Variant KIF1C:c.720+19_720+20delCC (chr17-5002851-GCC-G) – ACMG Classification: Benign (-16 pts)

Variant summary

Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP6_Very_StrongBA1

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

Scores

Not classified

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:3

Conservation

PhyloP100: 2.04

Variant links:

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 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -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 id 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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
KIF1C	NM_006612.6 link	c.720+19_720+20delCC		intron_variant	Intron 8 of 22	ENST00000320785.10	NP_006603.2	O43896
KIF1C	XM_005256424.3 link	c.720+19_720+20delCC		intron_variant	Intron 9 of 23		XP_005256481.1	O43896

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
KIF1C	ENST00000320785.10 link	c.720+10_720+11delCC		intron_variant	Intron 8 of 22	1	NM_006612.6	ENSP00000320821.5		O43896

Frequencies

GnomAD3 genomes

AF:

0.364

AC:

49848

AN:

137048

Hom.:

10183

Cov.:

show subpopulations

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

GnomAD4 exome

AF:

0.297

AC:

381157

AN:

1282924

Hom.:

53961

AF XY:

0.294

AC XY:

188397

AN XY:

641236

show subpopulations

Gnomad4 AFR exome

AF:

0.619

Gnomad4 AMR exome

AF:

0.269

Gnomad4 ASJ exome

AF:

0.289

Gnomad4 EAS exome

AF:

0.338

Gnomad4 SAS exome

AF:

0.211

Gnomad4 FIN exome

AF:

0.372

Gnomad4 NFE exome

AF:

0.288

Gnomad4 OTH exome

AF:

0.317

GnomAD4 genome

AF:

0.364

AC:

49886

AN:

137122

Hom.:

10190

Cov.:

AF XY:

0.366

AC XY:

24091

AN XY:

65910

show subpopulations

Gnomad4 AFR

AF:

0.591

Gnomad4 AMR

AF:

0.297

Gnomad4 ASJ

AF:

0.274

Gnomad4 EAS

AF:

0.283

Gnomad4 SAS

AF:

0.206

Gnomad4 FIN

AF:

0.353

Gnomad4 NFE

AF:

0.274

Gnomad4 OTH

AF:

0.360

ClinVar

Significance: Benign

Submissions summary: Benign:3

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Mar 08, 2016

GeneDx

Significance: Benign

Review Status: flagged submission

Collection Method: clinical testing

- -

May 29, 2018

GeneDx

Significance: Benign

Review Status: criteria provided, single submitter

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 v4.3

Name

Calibrated prediction

Score

Prediction

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

17-5002851-GCCCC-GCC

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over