rs211291

Positions:

• chr10-32047831-A-G
• chr10-32047831-A-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_004521.3(KIF5B):​c.214+633T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.2 in 152,218 control chromosomes in the GnomAD database, including 3,290 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 0.20 (3290 hom., cov: 32)
• Consequence: KIF5B NM_004521.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.78

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=-0.84).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.242 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
KIF5B	NM_004521.3	c.214+633T>C		intron_variant		ENST00000302418.5	NP_004512.1
KIF5B	XM_047425202.1	c.214+633T>C		intron_variant			XP_047281158.1
KIF5B	XM_047425203.1	c.-69+633T>C		intron_variant			XP_047281159.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
KIF5B	ENST00000302418.5	c.214+633T>C		intron_variant		1	NM_004521.3	ENSP00000307078	P1

Frequencies

GnomAD3 genomes AF: 0.200 AC: 30355 AN: 152100 Hom.: 3282 Cov.: 32

Gnomad AFR AF: 0.160

Gnomad AMI AF: 0.180

Gnomad AMR AF: 0.182

Gnomad ASJ AF: 0.235

Gnomad EAS AF: 0.00788

Gnomad SAS AF: 0.179

Gnomad FIN AF: 0.182

Gnomad MID AF: 0.218

Gnomad NFE AF: 0.245

Gnomad OTH AF: 0.201

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

GnomAD4 genome AF: 0.200 AC: 30399 AN: 152218 Hom.: 3290 Cov.: 32 AF XY: 0.196 AC XY: 14559 AN XY: 74416

Gnomad4 AFR AF: 0.160

Gnomad4 AMR AF: 0.182

Gnomad4 ASJ AF: 0.235

Gnomad4 EAS AF: 0.00770

Gnomad4 SAS AF: 0.178

Gnomad4 FIN AF: 0.182

Gnomad4 NFE AF: 0.245

Gnomad4 OTH AF: 0.204

Alfa AF: 0.212 Hom.: 436

Bravo AF: 0.200

Asia WGS AF: 0.122 AC: 426 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	15
DANN	Benign	0.82

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: rs211291; hg19: chr10-32336759;