10-89751702-A-G

Variant names:

• chr10-89751702-A-G
• rs2077946
• NM_001284259.2:c.4222+231A>G

Variant summary

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

The NM_001284259.2(KIF20B):​c.4222+231A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.309 in 151,736 control chromosomes in the GnomAD database, including 8,128 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 (8128 hom., cov: 32)
• Consequence: KIF20B NM_001284259.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.640
• Publications: 3 publications found

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

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.456 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001284259.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	KIF20B	NM_001284259.2	MANE Select	c.4222+231A>G		intron	N/A	NP_001271188.1	Q96Q89-1
	KIF20B	NM_016195.4		c.4102+231A>G		intron	N/A	NP_057279.2
	KIF20B	NM_001382506.1		c.4009+231A>G		intron	N/A	NP_001369435.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	KIF20B	ENST00000371728.8	TSL:1 MANE Select	c.4222+231A>G		intron	N/A	ENSP00000360793.3	Q96Q89-1
	KIF20B	ENST00000260753.8	TSL:1	c.4102+231A>G		intron	N/A	ENSP00000260753.4	Q96Q89-3
	KIF20B	ENST00000478929.1	TSL:1	n.2768+231A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.309 AC: 46786 AN: 151618 Hom.: 8104 Cov.: 32

Gnomad AFR AF: 0.461

Gnomad AMI AF: 0.162

Gnomad AMR AF: 0.259

Gnomad ASJ AF: 0.307

Gnomad EAS AF: 0.304

Gnomad SAS AF: 0.448

Gnomad FIN AF: 0.244

Gnomad MID AF: 0.244

Gnomad NFE AF: 0.231

Gnomad OTH AF: 0.261

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

GnomAD4 genome AF: 0.309 AC: 46841 AN: 151736 Hom.: 8128 Cov.: 32 AF XY: 0.311 AC XY: 23056 AN XY: 74158

African (AFR) AF: 0.461 AC: 19070 AN: 41358

American (AMR) AF: 0.259 AC: 3952 AN: 15246

Ashkenazi Jewish (ASJ) AF: 0.307 AC: 1064 AN: 3466

East Asian (EAS) AF: 0.304 AC: 1572 AN: 5174

South Asian (SAS) AF: 0.448 AC: 2153 AN: 4808

European-Finnish (FIN) AF: 0.244 AC: 2575 AN: 10548

Middle Eastern (MID) AF: 0.231 AC: 68 AN: 294

European-Non Finnish (NFE) AF: 0.231 AC: 15671 AN: 67822

Other (OTH) AF: 0.270 AC: 569 AN: 2110

Alfa AF: 0.286 Hom.: 1061

Bravo AF: 0.309

Asia WGS AF: 0.408 AC: 1418 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	2.5
DANN	Benign	0.67
PhyloP100		0.64
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: rs2077946; hg19: chr10-91511459;