Variant rs6738277 details in Genebe, Genetics Data Aggregator

Variant summary

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

The NM_004522.3(KIF5C):c.2100+106A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.65 in 1,558,242 control chromosomes in the GnomAD database, including 333,063 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.68 ( 35594 hom., cov: 32)

Exomes 𝑓: 0.65 ( 297469 hom. )

Consequence

KIF5C
NM_004522.3 intron

Scores

Clinical Significance

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

Conservation

PhyloP100: -0.0820

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:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.9).

BP6

Variant 2-148997446-A-G is Benign according to our data. Variant chr2-148997446-A-G is described in ClinVar as [Benign]. Clinvar id is 1240665.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.769 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
KIF5C	NM_004522.3 linkuse as main transcript	c.2100+106A>G		intron_variant		ENST00000435030.6	NP_004513.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
KIF5C	ENST00000435030.6 linkuse as main transcript	c.2100+106A>G		intron_variant		1	NM_004522.3	ENSP00000393379	P4	O60282-1

Frequencies

GnomAD3 genomes

AF:

0.678

AC:

103051

AN:

151908

Hom.:

35545

Cov.:

show subpopulations

Gnomad AFR

AF:

0.776

Gnomad AMI

AF:

0.591

Gnomad AMR

AF:

0.667

Gnomad ASJ

AF:

0.727

Gnomad EAS

AF:

0.307

Gnomad SAS

AF:

0.668

Gnomad FIN

AF:

0.647

Gnomad MID

AF:

0.737

Gnomad NFE

AF:

0.653

Gnomad OTH

AF:

0.686

GnomAD3 exomes

AF:

0.638

AC:

118459

AN:

185594

Hom.:

38799

AF XY:

0.643

AC XY:

63528

AN XY:

98776

show subpopulations

Gnomad AFR exome

AF:

0.790

Gnomad AMR exome

AF:

0.604

Gnomad ASJ exome

AF:

0.707

Gnomad EAS exome

AF:

0.292

Gnomad SAS exome

AF:

0.687

Gnomad FIN exome

AF:

0.662

Gnomad NFE exome

AF:

0.657

Gnomad OTH exome

AF:

0.664

GnomAD4 exome

AF:

0.647

AC:

909943

AN:

1406216

Hom.:

297469

Cov.:

AF XY:

0.649

AC XY:

449973

AN XY:

692924

show subpopulations

Gnomad4 AFR exome

AF:

0.788

Gnomad4 AMR exome

AF:

0.611

Gnomad4 ASJ exome

AF:

0.719

Gnomad4 EAS exome

AF:

0.336

Gnomad4 SAS exome

AF:

0.690

Gnomad4 FIN exome

AF:

0.663

Gnomad4 NFE exome

AF:

0.649

Gnomad4 OTH exome

AF:

0.647

GnomAD4 genome

AF:

0.679

AC:

103158

AN:

152026

Hom.:

35594

Cov.:

AF XY:

0.675

AC XY:

50159

AN XY:

74292

show subpopulations

Gnomad4 AFR

AF:

0.776

Gnomad4 AMR

AF:

0.668

Gnomad4 ASJ

AF:

0.727

Gnomad4 EAS

AF:

0.307

Gnomad4 SAS

AF:

0.669

Gnomad4 FIN

AF:

0.647

Gnomad4 NFE

AF:

0.653

Gnomad4 OTH

AF:

0.682

Alfa

AF:

0.667

Hom.:

38895

Bravo

AF:

0.680

Asia WGS

AF:

0.544

AC:

1890

AN:

3476

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	clinical testing	GeneDx	Jun 26, 2018	- -
Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.90

CADD

Benign

1.4

DANN

Benign

0.39

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