chr10-32047831-A-G

Variant names:

• chr10-32047831-A-G
• rs211291
• NM_004521.3:c.214+633T>C

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 0 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=-0.84).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.242 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_004521.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	KIF5B	NM_004521.3	MANE Select	c.214+633T>C		intron	N/A	NP_004512.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	KIF5B	ENST00000302418.5	TSL:1 MANE Select	c.214+633T>C		intron	N/A	ENSP00000307078.4

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

African (AFR) AF: 0.160 AC: 6659 AN: 41530

American (AMR) AF: 0.182 AC: 2784 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.235 AC: 814 AN: 3470

East Asian (EAS) AF: 0.00770 AC: 40 AN: 5192

South Asian (SAS) AF: 0.178 AC: 861 AN: 4824

European-Finnish (FIN) AF: 0.182 AC: 1931 AN: 10594

Middle Eastern (MID) AF: 0.228 AC: 67 AN: 294

European-Non Finnish (NFE) AF: 0.245 AC: 16648 AN: 67996

Other (OTH) AF: 0.204 AC: 431 AN: 2116

Alfa AF: 0.211 Hom.: 450

Bravo AF: 0.200

Asia WGS AF: 0.122 AC: 426 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	15
DANN	Benign	0.82
PhyloP100		1.8
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: rs211291; hg19: chr10-32336759;