Genetic Variant NM_006612.6:c.720+19_720+20dupCC (chr17-5002851-G-GCC) – ACMG Classification: Uncertain_significance (0 pts)

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 0P and 0B.

The NM_006612.6(KIF1C):c.720+19_720+20dupCC variant causes a intron change involving the alteration of a non-conserved nucleotide. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.000058 ( 0 hom., cov: 0)

Exomes 𝑓: 0.00036 ( 0 hom. )

Consequence

KIF1C
NM_006612.6 intron

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 2.04

Publications

1 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 Gene-Disease associations (from GenCC):

spastic ataxia 2
Inheritance: AR, AD Classification: STRONG, MODERATE, SUPPORTIVE Submitted by: Labcorp Genetics (formerly Invitae), Ambry Genetics, Orphanet

KIF1C links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Uncertain_significance. The variant received 0 ACMG points.

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

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

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
KIF1C	ENST00000320785.10	TSL:1 MANE Select	c.720+9_720+10insCC	intron	N/A	ENSP00000320821.5	O43896
KIF1C	ENST00000948910.1		c.720+9_720+10insCC	intron	N/A	ENSP00000618969.1
KIF1C	ENST00000948913.1		c.720+9_720+10insCC	intron	N/A	ENSP00000618972.1

Frequencies

GnomAD3 genomes

AF:

0.0000584

AC:

AN:

137018

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0000277

Gnomad AMI

AF:

0.00115

Gnomad AMR

AF:

0.00

Gnomad ASJ

AF:

0.000302

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.0000779

Gnomad OTH

AF:

0.00

GnomAD2 exomes

AF:

0.000316

AC:

AN:

193244

AF XY:

0.000228

show subpopulations

Gnomad AFR exome

AF:

0.0000684

Gnomad AMR exome

AF:

0.000629

Gnomad ASJ exome

AF:

0.000269

Gnomad EAS exome

AF:

0.000561

Gnomad FIN exome

AF:

0.00

Gnomad NFE exome

AF:

0.000156

Gnomad OTH exome

AF:

0.00

GnomAD4 exome

AF:

0.000364

AC:

468

AN:

1284384

Hom.:

Cov.:

AF XY:

0.000397

AC XY:

255

AN XY:

641916

show subpopulations

⚠️ The allele balance in gnomAD version 4 Exomes is significantly skewed from the expected value of 0.5.

African (AFR)

AF:

0.0000321

AC:

AN:

31164

American (AMR)

AF:

0.000442

AC:

AN:

40708

Ashkenazi Jewish (ASJ)

AF:

0.000256

AC:

AN:

23446

East Asian (EAS)

AF:

0.000413

AC:

AN:

36352

South Asian (SAS)

AF:

0.00197

AC:

153

AN:

77638

European-Finnish (FIN)

AF:

0.000108

AC:

AN:

46302

Middle Eastern (MID)

AF:

0.00

AC:

AN:

4002

European-Non Finnish (NFE)

AF:

0.000248

AC:

241

AN:

971166

Other (OTH)

AF:

0.000541

AC:

AN:

53606

⚠️ The allele balance in gnomAD4 Exomes is highly skewed from 0.5 (p-value = 0), which strongly suggests a high chance of mosaicism in these individuals.

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.271

Heterozygous variant carriers

147

196

245

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Variant carriers

<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:

0.0000584

AC:

AN:

137092

Hom.:

Cov.:

AF XY:

0.0000759

AC XY:

AN XY:

65894

show subpopulations

African (AFR)

AF:

0.0000276

AC:

AN:

36240

American (AMR)

AF:

0.00

AC:

AN:

13528

Ashkenazi Jewish (ASJ)

AF:

0.000302

AC:

AN:

3312

East Asian (EAS)

AF:

0.00

AC:

AN:

4526

South Asian (SAS)

AF:

0.00

AC:

AN:

4086

European-Finnish (FIN)

AF:

0.00

AC:

AN:

8244

Middle Eastern (MID)

AF:

0.00

AC:

AN:

282

European-Non Finnish (NFE)

AF:

0.0000779

AC:

AN:

64144

Other (OTH)

AF:

0.00

AC:

AN:

1862

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.438

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Alfa

AF:

0.00

Hom.:

580

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

PhyloP100

2.0

Mutation Taster

=100/0

polymorphism

(source)

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over