rs1251363

Variant names:

• chr10-32039598-G-C
• rs1251363
• NM_004521.3:c.289-167C>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_004521.3(KIF5B):​c.289-167C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.471 in 151,912 control chromosomes in the GnomAD database, including 17,412 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 0.47 (17412 hom., cov: 32)
• Consequence: KIF5B NM_004521.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.132
• Publications: 7 publications found

Genes affected

KIF5B (HGNC:6324): (kinesin family member 5B) Enables identical protein binding activity; microtubule binding activity; and microtubule motor activity. Involved in several processes, including lysosome localization; natural killer cell mediated cytotoxicity; and positive regulation of protein localization to plasma membrane. Located in centriolar satellite; cytosol; and vesicle. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.593 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
KIF5B	NM_004521.3	c.289-167C>G		intron_variant	Intron 3 of 25	ENST00000302418.5	NP_004512.1
KIF5B	XM_047425202.1	c.289-167C>G		intron_variant	Intron 3 of 24		XP_047281158.1
KIF5B	XM_047425203.1	c.7-167C>G		intron_variant	Intron 4 of 26		XP_047281159.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
KIF5B	ENST00000302418.5	c.289-167C>G		intron_variant	Intron 3 of 25	1	NM_004521.3	ENSP00000307078.4

Frequencies

GnomAD3 genomes AF: 0.471 AC: 71451 AN: 151794 Hom.: 17410 Cov.: 32

Gnomad AFR AF: 0.351

Gnomad AMI AF: 0.538

Gnomad AMR AF: 0.479

Gnomad ASJ AF: 0.472

Gnomad EAS AF: 0.610

Gnomad SAS AF: 0.495

Gnomad FIN AF: 0.598

Gnomad MID AF: 0.462

Gnomad NFE AF: 0.509

Gnomad OTH AF: 0.472

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

GnomAD4 genome AF: 0.471 AC: 71477 AN: 151912 Hom.: 17412 Cov.: 32 AF XY: 0.475 AC XY: 35288 AN XY: 74234

African (AFR) AF: 0.351 AC: 14533 AN: 41416

American (AMR) AF: 0.478 AC: 7298 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.472 AC: 1636 AN: 3468

East Asian (EAS) AF: 0.611 AC: 3159 AN: 5172

South Asian (SAS) AF: 0.496 AC: 2392 AN: 4822

European-Finnish (FIN) AF: 0.598 AC: 6310 AN: 10550

Middle Eastern (MID) AF: 0.466 AC: 137 AN: 294

European-Non Finnish (NFE) AF: 0.509 AC: 34530 AN: 67894

Other (OTH) AF: 0.470 AC: 991 AN: 2110

Alfa AF: 0.493 Hom.: 2318

Bravo AF: 0.456

Asia WGS AF: 0.517 AC: 1789 AN: 3466

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.97
DANN	Benign	0.63
PhyloP100		-0.13
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1
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: rs1251363; hg19: chr10-32328526;