Variant 10-89727892-A-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_001284259.2(KIF20B):c.2267A>T(p.Asn756Ile) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.204 in 1,536,074 control chromosomes in the GnomAD database, including 34,622 homozygotes. In-silico tool predicts a benign outcome for this variant. 12/20 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.

Frequency

Genomes: 𝑓 0.18 ( 3136 hom., cov: 32)

Exomes 𝑓: 0.21 ( 31486 hom. )

Consequence

KIF20B
NM_001284259.2 missense

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.336

Variant links:

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]

KIF20B links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.00417462).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.335 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
KIF20B	NM_001284259.2 linkuse as main transcript	c.2267A>T	p.Asn756Ile	missense_variant	17/33	ENST00000371728.8	NP_001271188.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
KIF20B	ENST00000371728.8 linkuse as main transcript	c.2267A>T	p.Asn756Ile	missense_variant	17/33	1	NM_001284259.2	ENSP00000360793	A2	Q96Q89-1
KIF20B	ENST00000260753.8 linkuse as main transcript	c.2147A>T	p.Asn716Ile	missense_variant	17/33	1		ENSP00000260753	P4	Q96Q89-3
KIF20B	ENST00000478929.1 linkuse as main transcript	n.813A>T		non_coding_transcript_exon_variant	4/20	1

Frequencies

GnomAD3 genomes

AF:

0.185

AC:

28116

AN:

152016

Hom.:

3139

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0730

Gnomad AMI

AF:

0.197

Gnomad AMR

AF:

0.188

Gnomad ASJ

AF:

0.199

Gnomad EAS

AF:

0.348

Gnomad SAS

AF:

0.216

Gnomad FIN

AF:

0.317

Gnomad MID

AF:

0.162

Gnomad NFE

AF:

0.216

Gnomad OTH

AF:

0.199

GnomAD3 exomes

AF:

0.217

AC:

51243

AN:

236060

Hom.:

5956

AF XY:

0.217

AC XY:

27756

AN XY:

128064

show subpopulations

Gnomad AFR exome

AF:

0.0702

Gnomad AMR exome

AF:

0.215

Gnomad ASJ exome

AF:

0.192

Gnomad EAS exome

AF:

0.326

Gnomad SAS exome

AF:

0.223

Gnomad FIN exome

AF:

0.304

Gnomad NFE exome

AF:

0.205

Gnomad OTH exome

AF:

0.220

GnomAD4 exome

AF:

0.206

AC:

285294

AN:

1383938

Hom.:

31486

Cov.:

AF XY:

0.206

AC XY:

141980

AN XY:

689156

show subpopulations

Gnomad4 AFR exome

AF:

0.0642

Gnomad4 AMR exome

AF:

0.209

Gnomad4 ASJ exome

AF:

0.179

Gnomad4 EAS exome

AF:

0.330

Gnomad4 SAS exome

AF:

0.218

Gnomad4 FIN exome

AF:

0.291

Gnomad4 NFE exome

AF:

0.202

Gnomad4 OTH exome

AF:

0.198

GnomAD4 genome

AF:

0.185

AC:

28109

AN:

152136

Hom.:

3136

Cov.:

AF XY:

0.191

AC XY:

14195

AN XY:

74376

show subpopulations

Gnomad4 AFR

AF:

0.0729

Gnomad4 AMR

AF:

0.188

Gnomad4 ASJ

AF:

0.199

Gnomad4 EAS

AF:

0.348

Gnomad4 SAS

AF:

0.215

Gnomad4 FIN

AF:

0.317

Gnomad4 NFE

AF:

0.216

Gnomad4 OTH

AF:

0.197

Alfa

AF:

0.209

Hom.:

2593

Bravo

AF:

0.170

TwinsUK

AF:

0.227

AC:

840

ALSPAC

AF:

0.203

AC:

781

ESP6500AA

AF:

0.0723

AC:

316

ESP6500EA

AF:

0.203

AC:

1737

ExAC

AF:

0.218

AC:

26433

Asia WGS

AF:

0.271

AC:

940

AN:

3466

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.18

BayesDel_addAF

Benign

-0.65

BayesDel_noAF

Benign

-0.57

CADD

Benign

DANN

Uncertain

0.98

DEOGEN2

Benign

0.012

.;T

Eigen

Benign

-0.32

Eigen_PC

Benign

-0.32

FATHMM_MKL

Benign

0.63

LIST_S2

Benign

0.48

T;T

MetaRNN

Benign

0.0042

T;T

MetaSVM

Benign

-0.92

MutationAssessor

Benign

2.0

.;M

MutationTaster

Benign

1.0

P;P;P;P

PrimateAI

Uncertain

0.49

PROVEAN

Benign

-1.9

N;N

REVEL

Benign

0.023

Sift

Benign

0.044

D;D

Sift4G

Benign

0.19

T;T

Polyphen

0.0030

B;D

Vest4

0.12

MPC

0.021

ClinPred

0.015

GERP RS

1.1

Varity_R

0.096

gMVP

0.10

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over