rs376647

chr17-5014050-G-Cchr17-5014050-G-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.539

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]

ACMG classification

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	c.1571+318G>C		intron_variant		ENST00000320785.10
KIF1C	XM_005256424.3	c.1571+318G>C		intron_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.0480 AC: 7298 AN: 152172 Hom.: 238 Cov.: 32

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

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.: 32 AF XY: 0.0490 AC XY: 3647 AN XY: 74470

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.: 17

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

Other links and lift over

dbSNP: rs376647; hg19: chr17-4917345; COSMIC: COSV57903613; COSMIC: COSV57903613;