17-5023565-C-A

Variant names:

Variant summary

Our verdict is Benign. The variant received -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_006612.6(KIF1C):c.2726C>A(p.Pro909Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00539 in 1,613,566 control chromosomes in the GnomAD database, including 402 homozygotes. In-silico tool predicts a benign outcome for this variant. 16/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★). Synonymous variant affecting the same amino acid position (i.e. P909P) has been classified as Likely benign.

Frequency

Genomes: 𝑓 0.030 ( 223 hom., cov: 32)

Exomes 𝑓: 0.0029 ( 179 hom. )

Consequence

KIF1C
NM_006612.6 missense

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:4

Conservation

PhyloP100: 1.10

Publications

0 publications found

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:

KIF1C-AS1 (HGNC:40324): (KIF1C antisense RNA 1)

KIF1C-AS1 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -20 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.002075553).

BP6

Variant 17-5023565-C-A is Benign according to our data. Variant chr17-5023565-C-A is described in CliVar as Benign. Clinvar id is 383663.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr17-5023565-C-A is described in CliVar as Benign. Clinvar id is 383663.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr17-5023565-C-A is described in CliVar as Benign. Clinvar id is 383663.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr17-5023565-C-A is described in CliVar as Benign. Clinvar id is 383663.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr17-5023565-C-A is described in CliVar as Benign. Clinvar id is 383663.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr17-5023565-C-A is described in CliVar as Benign. Clinvar id is 383663.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr17-5023565-C-A is described in CliVar as Benign. Clinvar id is 383663.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr17-5023565-C-A is described in CliVar as Benign. Clinvar id is 383663.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr17-5023565-C-A is described in CliVar as Benign. Clinvar id is 383663.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr17-5023565-C-A is described in CliVar as Benign. Clinvar id is 383663.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr17-5023565-C-A is described in CliVar as Benign. Clinvar id is 383663.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr17-5023565-C-A is described in CliVar as Benign. Clinvar id is 383663.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr17-5023565-C-A is described in CliVar as Benign. Clinvar id is 383663.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr17-5023565-C-A is described in CliVar as Benign. Clinvar id is 383663.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr17-5023565-C-A is described in CliVar as Benign. Clinvar id is 383663.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr17-5023565-C-A is described in CliVar as Benign. Clinvar id is 383663.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr17-5023565-C-A is described in CliVar as Benign. Clinvar id is 383663.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr17-5023565-C-A is described in CliVar as Benign. Clinvar id is 383663.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr17-5023565-C-A is described in CliVar as Benign. Clinvar id is 383663.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr17-5023565-C-A is described in CliVar as Benign. Clinvar id is 383663.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr17-5023565-C-A is described in CliVar as Benign. Clinvar id is 383663.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr17-5023565-C-A is described in CliVar as Benign. Clinvar id is 383663.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr17-5023565-C-A is described in CliVar as Benign. Clinvar id is 383663.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr17-5023565-C-A is described in CliVar as Benign. Clinvar id is 383663.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr17-5023565-C-A is described in CliVar as Benign. Clinvar id is 383663.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr17-5023565-C-A is described in CliVar as Benign. Clinvar id is 383663.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr17-5023565-C-A is described in CliVar as Benign. Clinvar id is 383663.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr17-5023565-C-A is described in CliVar as Benign. Clinvar id is 383663.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr17-5023565-C-A is described in CliVar as Benign. Clinvar id is 383663.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr17-5023565-C-A is described in CliVar as Benign. Clinvar id is 383663.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr17-5023565-C-A is described in CliVar as Benign. Clinvar id is 383663.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.101 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
KIF1C	NM_006612.6 link	c.2726C>A	p.Pro909Gln	missense_variant	Exon 23 of 23	ENST00000320785.10	NP_006603.2	O43896
KIF1C	XM_005256424.3 link	c.2726C>A	p.Pro909Gln	missense_variant	Exon 24 of 24		XP_005256481.1	O43896

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
KIF1C	ENST00000320785.10 link	c.2726C>A	p.Pro909Gln	missense_variant	Exon 23 of 23	1	NM_006612.6	ENSP00000320821.5		O43896
KIF1C-AS1	ENST00000438266.2 link	n.172-2610G>T		intron_variant	Intron 1 of 3	2

Frequencies

GnomAD3 genomes

AF:

0.0295

AC:

4488

AN:

152060

Hom.:

223

Cov.:

show subpopulations

Gnomad AFR

AF:

0.103

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00969

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.000827

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00316

Gnomad NFE

AF:

0.000235

Gnomad OTH

AF:

0.0191

GnomAD2 exomes

AF:

0.00819

AC:

2028

AN:

247538

AF XY:

0.00614

show subpopulations

Gnomad AFR exome

AF:

0.109

Gnomad AMR exome

AF:

0.00705

Gnomad ASJ exome

AF:

0.00

Gnomad EAS exome

AF:

0.00

Gnomad FIN exome

AF:

0.00

Gnomad NFE exome

AF:

0.000154

Gnomad OTH exome

AF:

0.00345

GnomAD4 exome

AF:

0.00288

AC:

4214

AN:

1461388

Hom.:

179

Cov.:

AF XY:

0.00245

AC XY:

1779

AN XY:

727010

show subpopulations

African (AFR)

AF:

0.101

AC:

3385

AN:

33480

American (AMR)

AF:

0.00718

AC:

321

AN:

44716

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

26122

East Asian (EAS)

AF:

0.00

AC:

AN:

39700

South Asian (SAS)

AF:

0.000116

AC:

AN:

86246

European-Finnish (FIN)

AF:

0.00

AC:

AN:

53114

Middle Eastern (MID)

AF:

0.00295

AC:

AN:

5764

European-Non Finnish (NFE)

AF:

0.0000935

AC:

104

AN:

1111876

Other (OTH)

AF:

0.00624

AC:

377

AN:

60370

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

244

488

733

977

1221

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

104

208

312

416

520

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.0295

AC:

4491

AN:

152178

Hom.:

223

Cov.:

AF XY:

0.0284

AC XY:

2115

AN XY:

74390

show subpopulations

African (AFR)

AF:

0.103

AC:

4283

AN:

41506

American (AMR)

AF:

0.00968

AC:

148

AN:

15286

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

3470

East Asian (EAS)

AF:

0.00

AC:

AN:

5154

South Asian (SAS)

AF:

0.000621

AC:

AN:

4832

European-Finnish (FIN)

AF:

0.00

AC:

AN:

10612

Middle Eastern (MID)

AF:

0.00340

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.000235

AC:

AN:

68000

Other (OTH)

AF:

0.0189

AC:

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.495

Heterozygous variant carriers

208

415

623

830

1038

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

100

150

200

250

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.0173

Hom.:

Bravo

AF:

0.0331

ESP6500AA

AF:

0.0992

AC:

437

ESP6500EA

AF:

0.00

AC:

ExAC

AF:

0.0101

AC:

1226

Asia WGS

AF:

0.00433

AC:

AN:

3478

EpiCase

AF:

0.000327

EpiControl

AF:

0.000178

ClinVar

Significance: Benign

Submissions summary: Benign:4

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not specified

Benign:1

Sep 26, 2016

GeneDx

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. -

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

May 14, 2021

Genome Diagnostics Laboratory, The Hospital for Sick Children

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

- -

not provided

Benign:1

Breakthrough Genomics, Breakthrough Genomics

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:not provided

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.081

BayesDel_addAF

Benign

-0.55

BayesDel_noAF

Benign

-0.47

CADD

Benign

(source)

DANN

Benign

0.90

DEOGEN2

Benign

0.080

Eigen

Benign

-0.39

Eigen_PC

Benign

-0.43

FATHMM_MKL

Benign

0.20

LIST_S2

Benign

0.64

MetaRNN

Benign

0.0021

MetaSVM

Benign

-1.1

MutationAssessor

Benign

0.69

PhyloP100

1.1

PrimateAI

Benign

0.46

PROVEAN

Benign

-0.070

REVEL

Benign

0.13

Sift

Benign

0.030

Sift4G

Uncertain

0.017

Polyphen

0.61

Vest4

0.087

MPC

0.34

ClinPred

0.011

GERP RS

4.9

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.1

Varity_R

0.035

gMVP

0.25

Mutation Taster

=98/2

polymorphism (auto)

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.0

Details are displayed if max score is > 0.2

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

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

Other links and lift over