Genetic Variant KIF1C:c.1751-30G>A (chr17-5020462-G-A) – ACMG Classification: Benign (-20 pts)

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_006612.6(KIF1C):c.1751-30G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0423 in 1,583,604 control chromosomes in the GnomAD database, including 1,893 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★). There are indicators that this mutation may affect the branch point..

Frequency

Genomes: 𝑓 0.064 ( 473 hom., cov: 32)

Exomes 𝑓: 0.040 ( 1420 hom. )

Consequence

KIF1C
NM_006612.6 intron

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: -2.06

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 -20 ACMG points.

BP4

This position, referring to a specific DNA site, is a probable branch point but is likely benign (scored 1 / 10, using the threshold of <=3). The score ranges from 0 to 10, with values ≤3 considered benign and >5 classified as pathogenic. Computational evidence support a benign effect (BayesDel_noAF=-0.85).

BP6

Variant 17-5020462-G-A is Benign according to our data. Variant chr17-5020462-G-A is described in ClinVar as [Benign]. Clinvar id is 1237107.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.134 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
KIF1C	NM_006612.6 link	c.1751-30G>A		intron_variant	Intron 19 of 22	ENST00000320785.10	NP_006603.2	O43896
KIF1C	XM_005256424.3 link	c.1751-30G>A		intron_variant	Intron 20 of 23		XP_005256481.1	O43896

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
KIF1C	ENST00000320785.10 link	c.1751-30G>A		intron_variant	Intron 19 of 22	1	NM_006612.6	ENSP00000320821.5		O43896
KIF1C	ENST00000573815.1 link	n.293-30G>A		intron_variant	Intron 3 of 5	5

Frequencies

GnomAD3 genomes

AF:

0.0635

AC:

9662

AN:

152104

Hom.:

474

Cov.:

show subpopulations

Gnomad AFR

AF:

0.137

Gnomad AMI

AF:

0.0274

Gnomad AMR

AF:

0.0300

Gnomad ASJ

AF:

0.0202

Gnomad EAS

AF:

0.00694

Gnomad SAS

AF:

0.0108

Gnomad FIN

AF:

0.0569

Gnomad MID

AF:

0.0285

Gnomad NFE

AF:

0.0382

Gnomad OTH

AF:

0.0575

GnomAD3 exomes

AF:

0.0372

AC:

8583

AN:

230796

Hom.:

289

AF XY:

0.0347

AC XY:

4341

AN XY:

125018

show subpopulations

Gnomad AFR exome

AF:

0.142

Gnomad AMR exome

AF:

0.0211

Gnomad ASJ exome

AF:

0.0197

Gnomad EAS exome

AF:

0.00702

Gnomad SAS exome

AF:

0.0104

Gnomad FIN exome

AF:

0.0561

Gnomad NFE exome

AF:

0.0361

Gnomad OTH exome

AF:

0.0361

GnomAD4 exome

AF:

0.0400

AC:

57279

AN:

1431382

Hom.:

1420

Cov.:

AF XY:

0.0389

AC XY:

27578

AN XY:

708852

show subpopulations

Gnomad4 AFR exome

AF:

0.136

Gnomad4 AMR exome

AF:

0.0212

Gnomad4 ASJ exome

AF:

0.0197

Gnomad4 EAS exome

AF:

0.00292

Gnomad4 SAS exome

AF:

0.0105

Gnomad4 FIN exome

AF:

0.0567

Gnomad4 NFE exome

AF:

0.0412

Gnomad4 OTH exome

AF:

0.0410

GnomAD4 genome

AF:

0.0635

AC:

9667

AN:

152222

Hom.:

473

Cov.:

AF XY:

0.0628

AC XY:

4673

AN XY:

74438

show subpopulations

Gnomad4 AFR

AF:

0.137

Gnomad4 AMR

AF:

0.0299

Gnomad4 ASJ

AF:

0.0202

Gnomad4 EAS

AF:

0.00696

Gnomad4 SAS

AF:

0.0108

Gnomad4 FIN

AF:

0.0569

Gnomad4 NFE

AF:

0.0382

Gnomad4 OTH

AF:

0.0578

Alfa

AF:

0.0483

Hom.:

Bravo

AF:

0.0647

Asia WGS

AF:

0.0220

AC:

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Breakthrough Genomics, Breakthrough Genomics

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: not provided

- -

Jun 26, 2018

GeneDx

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.85

CADD

Benign

0.11

DANN

Benign

0.45

BranchPoint Hunter

1.0

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.020

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

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over