rs10456809

Variant names:

• chr6-17813594-C-T
• rs10456809
• NM_022113.6:c.2000+3426G>A

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 12 publications found

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

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
KIF13A	NM_022113.6	c.2000+3426G>A		intron_variant	Intron 17 of 38	ENST00000259711.11	NP_071396.4
KIF13A	NM_001105566.3	c.2000+3426G>A		intron_variant	Intron 17 of 37		NP_001099036.1
KIF13A	NM_001105567.3	c.2000+3426G>A		intron_variant	Intron 17 of 36		NP_001099037.1
KIF13A	NM_001105568.4	c.2000+3426G>A		intron_variant	Intron 17 of 37		NP_001099038.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
KIF13A	ENST00000259711.11	c.2000+3426G>A		intron_variant	Intron 17 of 38	1	NM_022113.6	ENSP00000259711.6

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

African (AFR) AF: 0.368 AC: 15227 AN: 41416

American (AMR) AF: 0.460 AC: 7028 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.363 AC: 1259 AN: 3468

East Asian (EAS) AF: 0.395 AC: 2040 AN: 5162

South Asian (SAS) AF: 0.471 AC: 2265 AN: 4810

European-Finnish (FIN) AF: 0.522 AC: 5495 AN: 10532

Middle Eastern (MID) AF: 0.374 AC: 110 AN: 294

European-Non Finnish (NFE) AF: 0.453 AC: 30765 AN: 67978

Other (OTH) AF: 0.412 AC: 870 AN: 2112

Alfa AF: 0.439 Hom.: 44133

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
PhyloP100		-1.4
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs10456809; hg19: chr6-17813825;