Variant rs376647 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_006612.6(KIF1C):c.1571+318G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0548 in 332,192 control chromosomes in the GnomAD database, including 766 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.048 ( 237 hom., cov: 32)

Exomes 𝑓: 0.061 ( 529 hom. )

Consequence

KIF1C
NM_006612.6 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.539

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:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.92).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.189 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
KIF1C	NM_006612.6 linkuse as main transcript	c.1571+318G>C		intron_variant		ENST00000320785.10
KIF1C	XM_005256424.3 linkuse as main transcript	c.1571+318G>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
KIF1C	ENST00000320785.10 linkuse as main transcript	c.1571+318G>C		intron_variant		1	NM_006612.6	P1

Frequencies

GnomAD3 genomes

AF:

0.0480

AC:

7298

AN:

152172

Hom.:

238

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0367

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.0413

Gnomad ASJ

AF:

0.0536

Gnomad EAS

AF:

0.199

Gnomad SAS

AF:

0.0992

Gnomad FIN

AF:

0.0254

Gnomad MID

AF:

0.0506

Gnomad NFE

AF:

0.0449

Gnomad OTH

AF:

0.0516

GnomAD4 exome

AF:

0.0607

AC:

10920

AN:

179902

Hom.:

529

AF XY:

0.0618

AC XY:

5749

AN XY:

93054

show subpopulations

Gnomad4 AFR exome

AF:

0.0389

Gnomad4 AMR exome

AF:

0.0402

Gnomad4 ASJ exome

AF:

0.0685

Gnomad4 EAS exome

AF:

0.230

Gnomad4 SAS exome

AF:

0.0869

Gnomad4 FIN exome

AF:

0.0316

Gnomad4 NFE exome

AF:

0.0459

Gnomad4 OTH exome

AF:

0.0552

GnomAD4 genome

AF:

0.0479

AC:

7291

AN:

152290

Hom.:

237

Cov.:

AF XY:

0.0490

AC XY:

3647

AN XY:

74470

show subpopulations

Gnomad4 AFR

AF:

0.0367

Gnomad4 AMR

AF:

0.0413

Gnomad4 ASJ

AF:

0.0536

Gnomad4 EAS

AF:

0.199

Gnomad4 SAS

AF:

0.0980

Gnomad4 FIN

AF:

0.0254

Gnomad4 NFE

AF:

0.0449

Gnomad4 OTH

AF:

0.0501

Alfa

AF:

0.0463

Hom.:

Bravo

AF:

0.0490

Asia WGS

AF:

0.127

AC:

442

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.92

CADD

Benign

0.12

DANN

Benign

0.54

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

LitVar

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

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over