chr10-32026867-G-A

Position:

• chr10-32026867-G-A

Variant summary

Our verdict is Benign. Variant got -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

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

Verdict is Benign. Variant got -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/exons	MANE	UniProt
KIF5B	NM_004521.3	c.1725+1561C>T		intron_variant		ENST00000302418.5
KIF5B	XM_047425202.1	c.1725+1561C>T		intron_variant
KIF5B	XM_047425203.1	c.1443+1561C>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
KIF5B	ENST00000302418.5	c.1725+1561C>T		intron_variant		1	NM_004521.3	P1

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

Gnomad4 AFR AF: 0.0976

Gnomad4 AMR AF: 0.246

Gnomad4 ASJ AF: 0.249

Gnomad4 EAS AF: 0.130

Gnomad4 SAS AF: 0.254

Gnomad4 FIN AF: 0.365

Gnomad4 NFE AF: 0.291

Gnomad4 OTH AF: 0.231

Alfa AF: 0.266 Hom.: 2706

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

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: rs1639134; hg19: chr10-32315795;