Variant rs3734234 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_ModerateBP7BA1

The NM_022113.6(KIF13A):c.3208C>T(p.Leu1070=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.428 in 1,609,990 control chromosomes in the GnomAD database, including 152,054 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 0.36 ( 11252 hom., cov: 31)

Exomes 𝑓: 0.44 ( 140802 hom. )

Consequence

KIF13A
NM_022113.6 synonymous

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 3.08

Variant links:

Genes affected

KIF13A (HGNC:14566): (kinesin family member 13A) This gene encodes a member of the kinesin family of microtubule-based motor proteins that function in the positioning of endosomes. This family member can direct mannose-6-phosphate receptor-containing vesicles from the trans-Golgi network to the plasma membrane, and it is necessary for the steady-state distribution of late endosomes/lysosomes. It is also required for the translocation of FYVE-CENT and TTC19 from the centrosome to the midbody during cytokinesis, and it plays a role in melanosome maturation. Alternative splicing of this gene results in multiple transcript variants. [provided by RefSeq, Aug 2011]

KIF13A links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -11 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.37).

BP7

Synonymous conserved (PhyloP=3.08 with no splicing effect.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.576 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein
KIF13A	NM_022113.6 linkuse as main transcript	c.3208C>T	p.Leu1070=	synonymous_variant	25/39	ENST00000259711.11	NP_071396.4
KIF13A	NM_001105566.3 linkuse as main transcript	c.3208C>T	p.Leu1070=	synonymous_variant	25/38		NP_001099036.1
KIF13A	NM_001105567.3 linkuse as main transcript	c.3208C>T	p.Leu1070=	synonymous_variant	25/37		NP_001099037.1
KIF13A	NM_001105568.4 linkuse as main transcript	c.3208C>T	p.Leu1070=	synonymous_variant	25/38		NP_001099038.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
KIF13A	ENST00000259711.11 linkuse as main transcript	c.3208C>T	p.Leu1070=	synonymous_variant	25/39	1	NM_022113.6	ENSP00000259711		Q9H1H9-1

Frequencies

GnomAD3 genomes

AF:

0.365

AC:

55319

AN:

151756

Hom.:

11256

Cov.:

show subpopulations

Gnomad AFR

AF:

0.179

Gnomad AMI

AF:

0.315

Gnomad AMR

AF:

0.423

Gnomad ASJ

AF:

0.409

Gnomad EAS

AF:

0.593

Gnomad SAS

AF:

0.376

Gnomad FIN

AF:

0.398

Gnomad MID

AF:

0.411

Gnomad NFE

AF:

0.438

Gnomad OTH

AF:

0.397

GnomAD3 exomes

AF:

0.418

AC:

104005

AN:

248690

Hom.:

22840

AF XY:

0.419

AC XY:

56555

AN XY:

134888

show subpopulations

Gnomad AFR exome

AF:

0.170

Gnomad AMR exome

AF:

0.418

Gnomad ASJ exome

AF:

0.410

Gnomad EAS exome

AF:

0.611

Gnomad SAS exome

AF:

0.369

Gnomad FIN exome

AF:

0.407

Gnomad NFE exome

AF:

0.438

Gnomad OTH exome

AF:

0.419

GnomAD4 exome

AF:

0.435

AC:

634290

AN:

1458114

Hom.:

140802

Cov.:

AF XY:

0.433

AC XY:

314088

AN XY:

725348

show subpopulations

Gnomad4 AFR exome

AF:

0.167

Gnomad4 AMR exome

AF:

0.421

Gnomad4 ASJ exome

AF:

0.409

Gnomad4 EAS exome

AF:

0.604

Gnomad4 SAS exome

AF:

0.365

Gnomad4 FIN exome

AF:

0.410

Gnomad4 NFE exome

AF:

0.446

Gnomad4 OTH exome

AF:

0.421

GnomAD4 genome

AF:

0.364

AC:

55336

AN:

151876

Hom.:

11252

Cov.:

AF XY:

0.367

AC XY:

27201

AN XY:

74210

show subpopulations

Gnomad4 AFR

AF:

0.179

Gnomad4 AMR

AF:

0.423

Gnomad4 ASJ

AF:

0.409

Gnomad4 EAS

AF:

0.593

Gnomad4 SAS

AF:

0.377

Gnomad4 FIN

AF:

0.398

Gnomad4 NFE

AF:

0.438

Gnomad4 OTH

AF:

0.395

Alfa

AF:

0.418

Hom.:

17576

Bravo

AF:

0.363

Asia WGS

AF:

0.460

AC:

1600

AN:

3478

EpiCase

AF:

0.422

EpiControl

AF:

0.434

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.37

CADD

Benign

8.4

DANN

Benign

0.78

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.010

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

Computational scores

Splicing

Publications

LitVar

Other links and lift over