rs1639134

Variant names:

• chr10-32026867-G-A
• rs1639134
• NM_004521.3:c.1725+1561C>T

Variant summary

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

The NM_004521.3(KIF5B):​c.1725+1561C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.23 in 152,032 control chromosomes in the GnomAD database, including 4,704 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 0.23 (4704 hom., cov: 32)
• Consequence: KIF5B NM_004521.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.06
• Publications: 3 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=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.288 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
KIF5B	NM_004521.3	c.1725+1561C>T		intron_variant	Intron 15 of 25	ENST00000302418.5	NP_004512.1
KIF5B	XM_047425202.1	c.1725+1561C>T		intron_variant	Intron 15 of 24		XP_047281158.1
KIF5B	XM_047425203.1	c.1443+1561C>T		intron_variant	Intron 16 of 26		XP_047281159.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
KIF5B	ENST00000302418.5	c.1725+1561C>T		intron_variant	Intron 15 of 25	1	NM_004521.3	ENSP00000307078.4

Frequencies

GnomAD3 genomes AF: 0.230 AC: 35000 AN: 151914 Hom.: 4705 Cov.: 32

Gnomad AFR AF: 0.0978

Gnomad AMI AF: 0.291

Gnomad AMR AF: 0.247

Gnomad ASJ AF: 0.249

Gnomad EAS AF: 0.130

Gnomad SAS AF: 0.254

Gnomad FIN AF: 0.365

Gnomad MID AF: 0.197

Gnomad NFE AF: 0.291

Gnomad OTH AF: 0.233

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

GnomAD4 genome AF: 0.230 AC: 34999 AN: 152032 Hom.: 4704 Cov.: 32 AF XY: 0.232 AC XY: 17269 AN XY: 74290

African (AFR) AF: 0.0976 AC: 4052 AN: 41510

American (AMR) AF: 0.246 AC: 3759 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.249 AC: 864 AN: 3466

East Asian (EAS) AF: 0.130 AC: 672 AN: 5170

South Asian (SAS) AF: 0.254 AC: 1221 AN: 4812

European-Finnish (FIN) AF: 0.365 AC: 3846 AN: 10526

Middle Eastern (MID) AF: 0.199 AC: 58 AN: 292

European-Non Finnish (NFE) AF: 0.291 AC: 19776 AN: 67974

Other (OTH) AF: 0.231 AC: 487 AN: 2110

Alfa AF: 0.269 Hom.: 3027

Bravo AF: 0.215

Asia WGS AF: 0.200 AC: 694 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	3.6
DANN	Benign	0.62
PhyloP100		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: rs1639134; hg19: chr10-32315795;