Variant 2-148875586-A-C details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_StrongBP6_Moderate

The NM_004522.3(KIF5C):c.-32A>C variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.0035 ( 0 hom., cov: 0)

Exomes 𝑓: 0.099 ( 0 hom. )

Failed GnomAD Quality Control

Consequence

KIF5C
NM_004522.3 5_prime_UTR

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.00100

Variant links:

Genes affected

KIF5C (HGNC:6325): (kinesin family member 5C) The protein encoded by this gene is a kinesin heavy chain subunit involved in the transport of cargo within the central nervous system. The encoded protein, which acts as a tetramer by associating with another heavy chain and two light chains, interacts with protein kinase CK2. Mutations in this gene have been associated with complex cortical dysplasia with other brain malformations-2. Two transcript variants, one protein-coding and the other non-protein coding, have been found for this gene. [provided by RefSeq, Jul 2015]

KIF5C links:

KIF5C-AS1 (HGNC:40325): (KIF5C antisense RNA 1)

KIF5C-AS1 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -6 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.63).

BP6

Variant 2-148875586-A-C is Benign according to our data. Variant chr2-148875586-A-C is described in ClinVar as [Benign]. Clinvar id is 1249855.Status of the report is criteria_provided_single_submitter, 1 stars.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	#exon/exons	MANE	Protein
KIF5C	NM_004522.3 linkuse as main transcript	c.-32A>C	5_prime_UTR_variant	1/26	ENST00000435030.6	NP_004513.1
KIF5C-AS1	XR_001739733.2 linkuse as main transcript	n.7732T>G	non_coding_transcript_exon_variant	4/4
KIF5C	XM_017004062.2 linkuse as main transcript	c.-32A>C	5_prime_UTR_variant	1/26		XP_016859551.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
KIF5C	ENST00000435030.6 linkuse as main transcript	c.-32A>C		5_prime_UTR_variant	1/26	1	NM_004522.3	ENSP00000393379	P4	O60282-1
KIF5C-AS1	ENST00000601658.5 linkuse as main transcript	n.676+1640T>G		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes

AF:

0.00

AC:

149

AN:

42452

Hom.:

Cov.:

FAILED QC

Gnomad AFR

AF:

0.00259

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00217

Gnomad ASJ

AF:

0.00560

Gnomad EAS

AF:

0.00101

Gnomad SAS

AF:

0.00240

Gnomad FIN

AF:

0.00685

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.00422

Gnomad OTH

AF:

0.00356

GnomAD3 exomes

AF:

0.0702

AC:

4358

AN:

62064

Hom.:

AF XY:

0.0664

AC XY:

2402

AN XY:

36188

show subpopulations

Gnomad AFR exome

AF:

0.0984

Gnomad AMR exome

AF:

0.212

Gnomad ASJ exome

AF:

0.0536

Gnomad EAS exome

AF:

0.208

Gnomad SAS exome

AF:

0.0890

Gnomad FIN exome

AF:

0.0220

Gnomad NFE exome

AF:

0.0480

Gnomad OTH exome

AF:

0.0789

GnomAD4 exome

Data not reliable, filtered out with message: AS_VQSR

AF:

0.0990

AC:

19870

AN:

200688

Hom.:

Cov.:

AF XY:

0.0958

AC XY:

10326

AN XY:

107826

show subpopulations

Gnomad4 AFR exome

AF:

0.121

Gnomad4 AMR exome

AF:

0.205

Gnomad4 ASJ exome

AF:

0.0756

Gnomad4 EAS exome

AF:

0.0699

Gnomad4 SAS exome

AF:

0.126

Gnomad4 FIN exome

AF:

0.0450

Gnomad4 NFE exome

AF:

0.0969

Gnomad4 OTH exome

AF:

0.0876

GnomAD4 genome

Data not reliable, filtered out with message: AS_VQSR

AF:

0.00351

AC:

149

AN:

42506

Hom.:

Cov.:

AF XY:

0.00333

AC XY:

AN XY:

21036

show subpopulations

Gnomad4 AFR

AF:

0.00258

Gnomad4 AMR

AF:

0.00216

Gnomad4 ASJ

AF:

0.00560

Gnomad4 EAS

AF:

0.00102

Gnomad4 SAS

AF:

0.00240

Gnomad4 FIN

AF:

0.00685

Gnomad4 NFE

AF:

0.00422

Gnomad4 OTH

AF:

0.00351

Alfa

AF:

0.00119

Hom.:

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Aug 05, 2019

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.63

CADD

Benign

DANN

Benign

0.80

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

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over