rs238237

chr17-4999663-G-A

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BA1

The NM_006612.6(KIF1C):c.-148-187G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.794 in 152,034 control chromosomes in the GnomAD database, including 48,759 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.79 (48759 hom., cov: 31)
• Consequence: KIF1C NM_006612.6 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 1.48

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 -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.7).
• BP6: Variant 17-4999663-G-A is Benign according to our data. Variant chr17-4999663-G-A is described in ClinVar as [Benign]. Clinvar id is 1526316.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.903 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
KIF1C	NM_006612.6	c.-148-187G>A		intron_variant		ENST00000320785.10
KIF1C	XM_005256424.3	c.-148-187G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
KIF1C	ENST00000320785.10	c.-148-187G>A		intron_variant		1	NM_006612.6	P1
KIF1C	ENST00000574165.1	c.-148-187G>A		intron_variant		5

Frequencies

GnomAD3 genomes AF: 0.794 AC: 120582 AN: 151916 Hom.: 48708 Cov.: 31

Gnomad AFR AF: 0.911

Gnomad AMI AF: 0.712

Gnomad AMR AF: 0.736

Gnomad ASJ AF: 0.720

Gnomad EAS AF: 0.476

Gnomad SAS AF: 0.501

Gnomad FIN AF: 0.701

Gnomad MID AF: 0.826

Gnomad NFE AF: 0.799

Gnomad OTH AF: 0.812

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.794 AC: 120696 AN: 152034 Hom.: 48759 Cov.: 31 AF XY: 0.782 AC XY: 58085 AN XY: 74292

Gnomad4 AFR AF: 0.911

Gnomad4 AMR AF: 0.736

Gnomad4 ASJ AF: 0.720

Gnomad4 EAS AF: 0.477

Gnomad4 SAS AF: 0.503

Gnomad4 FIN AF: 0.701

Gnomad4 NFE AF: 0.799

Gnomad4 OTH AF: 0.810

Alfa AF: 0.806 Hom.: 8667

Bravo AF: 0.805

Asia WGS AF: 0.540 AC: 1881 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Mar 28, 2022

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.70
Cadd	Benign	14
Dann	Benign	0.56

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: rs238237; hg19: chr17-4902958; COSMIC: COSV57903586; COSMIC: COSV57903586;