rs10456809

chr6-17813594-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_022113.6(KIF13A):c.2000+3426G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.43 in 151,952 control chromosomes in the GnomAD database, including 14,232 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 0.43 (14232 hom., cov: 32)
• Consequence: KIF13A NM_022113.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.35

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.455 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
KIF13A	NM_022113.6	c.2000+3426G>A		intron_variant		ENST00000259711.11
KIF13A	NM_001105566.3	c.2000+3426G>A		intron_variant
KIF13A	NM_001105567.3	c.2000+3426G>A		intron_variant
KIF13A	NM_001105568.4	c.2000+3426G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
KIF13A	ENST00000259711.11	c.2000+3426G>A		intron_variant		1	NM_022113.6

Frequencies

GnomAD3 genomes AF: 0.430 AC: 65328 AN: 151834 Hom.: 14224 Cov.: 32

Gnomad AFR AF: 0.368

Gnomad AMI AF: 0.354

Gnomad AMR AF: 0.460

Gnomad ASJ AF: 0.363

Gnomad EAS AF: 0.395

Gnomad SAS AF: 0.473

Gnomad FIN AF: 0.522

Gnomad MID AF: 0.361

Gnomad NFE AF: 0.453

Gnomad OTH AF: 0.408

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

GnomAD4 genome AF: 0.430 AC: 65382 AN: 151952 Hom.: 14232 Cov.: 32 AF XY: 0.435 AC XY: 32330 AN XY: 74274

Gnomad4 AFR AF: 0.368

Gnomad4 AMR AF: 0.460

Gnomad4 ASJ AF: 0.363

Gnomad4 EAS AF: 0.395

Gnomad4 SAS AF: 0.471

Gnomad4 FIN AF: 0.522

Gnomad4 NFE AF: 0.453

Gnomad4 OTH AF: 0.412

Alfa AF: 0.444 Hom.: 29072

Bravo AF: 0.419

Asia WGS AF: 0.442 AC: 1536 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	0.43
Dann	Benign	0.53

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: rs10456809; hg19: chr6-17813825; COSMIC: COSV52441477;