rs3734234

chr6-17794263-G-Achr6-17794263-G-Cchr6-17794263-G-T

Variant summary

Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_Moderate BP7 BA1

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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 3.08

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 -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	UniProt
KIF13A	NM_022113.6	c.3208C>T	p.Leu1070=	synonymous_variant	25/39	ENST00000259711.11
KIF13A	NM_001105566.3	c.3208C>T	p.Leu1070=	synonymous_variant	25/38
KIF13A	NM_001105567.3	c.3208C>T	p.Leu1070=	synonymous_variant	25/37
KIF13A	NM_001105568.4	c.3208C>T	p.Leu1070=	synonymous_variant	25/38

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
KIF13A	ENST00000259711.11	c.3208C>T	p.Leu1070=	synonymous_variant	25/39	1	NM_022113.6

Frequencies

GnomAD3 genomes AF: 0.365 AC: 55319 AN: 151756 Hom.: 11256 Cov.: 31

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

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.: 34 AF XY: 0.433 AC XY: 314088 AN XY: 725348

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.: 31 AF XY: 0.367 AC XY: 27201 AN XY: 74210

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

Other links and lift over

dbSNP: rs3734234; hg19: chr6-17794494; COSMIC: COSV52451494;