10-89769101-C-T

Variant names:

• chr10-89769101-C-T
• rs962524
• NM_001284259.2:c.5242+213C>T

Variant summary

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

The NM_001284259.2(KIF20B):​c.5242+213C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.307 in 151,712 control chromosomes in the GnomAD database, including 7,974 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 0.31 (7974 hom., cov: 31)
• Consequence: KIF20B NM_001284259.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.231

Genes affected

KIF20B (HGNC:7212): (kinesin family member 20B) Enables several functions, including WW domain binding activity; plus-end-directed microtubule motor activity; and protein homodimerization activity. Involved in positive regulation of cell population proliferation and positive regulation of cytokinesis. Located in several cellular components, including microtubule cytoskeleton; midbody; and nuclear lumen. [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=-0.76).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.448 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
KIF20B	NM_001284259.2	c.5242+213C>T		intron_variant	Intron 31 of 32	ENST00000371728.8	NP_001271188.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
KIF20B	ENST00000371728.8	c.5242+213C>T		intron_variant	Intron 31 of 32	1	NM_001284259.2	ENSP00000360793.3
KIF20B	ENST00000260753.8	c.5122+213C>T		intron_variant	Intron 31 of 32	1		ENSP00000260753.4
KIF20B	ENST00000478929.1	n.3788+213C>T		intron_variant	Intron 18 of 19	1

Frequencies

GnomAD3 genomes AF: 0.306 AC: 46462 AN: 151592 Hom.: 7951 Cov.: 31

Gnomad AFR AF: 0.454

Gnomad AMI AF: 0.162

Gnomad AMR AF: 0.259

Gnomad ASJ AF: 0.308

Gnomad EAS AF: 0.303

Gnomad SAS AF: 0.447

Gnomad FIN AF: 0.245

Gnomad MID AF: 0.244

Gnomad NFE AF: 0.231

Gnomad OTH AF: 0.259

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

GnomAD4 genome AF: 0.307 AC: 46516 AN: 151712 Hom.: 7974 Cov.: 31 AF XY: 0.309 AC XY: 22894 AN XY: 74148

Gnomad4 AFR AF: 0.454

Gnomad4 AMR AF: 0.259

Gnomad4 ASJ AF: 0.308

Gnomad4 EAS AF: 0.303

Gnomad4 SAS AF: 0.447

Gnomad4 FIN AF: 0.245

Gnomad4 NFE AF: 0.231

Gnomad4 OTH AF: 0.267

Alfa AF: 0.272 Hom.: 1048

Bravo AF: 0.306

Asia WGS AF: 0.409 AC: 1420 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.76
CADD	Benign	7.6
DANN	Benign	0.81

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: rs962524; hg19: chr10-91528858;