rs2418929

Variant names:

• chr10-89741720-C-G
• rs2418929
• NM_001284259.2:c.3916-2088C>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.3916-2088C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.185 in 152,078 control chromosomes in the GnomAD database, including 3,134 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 0.18 (3134 hom., cov: 32)
• Consequence: KIF20B NM_001284259.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.281
• Publications: 6 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 (EAS) allele frequency at 95% confidence interval = 0.334 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
KIF20B	NM_001284259.2	c.3916-2088C>G		intron_variant	Intron 21 of 32	ENST00000371728.8	NP_001271188.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
KIF20B	ENST00000371728.8	c.3916-2088C>G		intron_variant	Intron 21 of 32	1	NM_001284259.2	ENSP00000360793.3
KIF20B	ENST00000260753.8	c.3796-2088C>G		intron_variant	Intron 21 of 32	1		ENSP00000260753.4
KIF20B	ENST00000478929.1	n.2462-2088C>G		intron_variant	Intron 8 of 19	1

Frequencies

GnomAD3 genomes AF: 0.185 AC: 28128 AN: 151958 Hom.: 3137 Cov.: 32

Gnomad AFR AF: 0.0726

Gnomad AMI AF: 0.197

Gnomad AMR AF: 0.188

Gnomad ASJ AF: 0.200

Gnomad EAS AF: 0.347

Gnomad SAS AF: 0.223

Gnomad FIN AF: 0.316

Gnomad MID AF: 0.165

Gnomad NFE AF: 0.216

Gnomad OTH AF: 0.199

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

GnomAD4 genome AF: 0.185 AC: 28120 AN: 152078 Hom.: 3134 Cov.: 32 AF XY: 0.191 AC XY: 14199 AN XY: 74328

African (AFR) AF: 0.0725 AC: 3008 AN: 41498

American (AMR) AF: 0.188 AC: 2869 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.200 AC: 693 AN: 3472

East Asian (EAS) AF: 0.347 AC: 1790 AN: 5158

South Asian (SAS) AF: 0.221 AC: 1067 AN: 4826

European-Finnish (FIN) AF: 0.316 AC: 3337 AN: 10550

Middle Eastern (MID) AF: 0.167 AC: 49 AN: 294

European-Non Finnish (NFE) AF: 0.216 AC: 14711 AN: 67972

Other (OTH) AF: 0.197 AC: 416 AN: 2114

Alfa AF: 0.202 Hom.: 434

Bravo AF: 0.170

Asia WGS AF: 0.277 AC: 962 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	5.4
DANN	Benign	0.60
PhyloP100		0.28
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: rs2418929; hg19: chr10-91501477;