Variant 10-89738497-A-G details in Genebe, Genetics Data Aggregator

Variant summary

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

The ENST00000371728.8(KIF20B):c.3656A>G(p.Asn1219Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.26 in 1,604,082 control chromosomes in the GnomAD database, including 58,824 homozygotes. In-silico tool predicts a benign outcome for this variant. 15/20 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 0.31 ( 8382 hom., cov: 33)

Exomes 𝑓: 0.25 ( 50442 hom. )

Consequence

KIF20B
ENST00000371728.8 missense

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.142

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:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=6.440282E-4).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.466 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.3656A>G	p.Asn1219Ser	missense_variant	20/33	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.3656A>G	p.Asn1219Ser	missense_variant	20/33	1	NM_001284259.2	ENSP00000360793	A2	Q96Q89-1
KIF20B	ENST00000260753.8 linkuse as main transcript	c.3536A>G	p.Asn1179Ser	missense_variant	20/33	1		ENSP00000260753	P4	Q96Q89-3
KIF20B	ENST00000478929.1 linkuse as main transcript	n.2202A>G		non_coding_transcript_exon_variant	7/20	1

Frequencies

GnomAD3 genomes

AF:

0.312

AC:

47364

AN:

151846

Hom.:

8355

Cov.:

show subpopulations

Gnomad AFR

AF:

0.472

Gnomad AMI

AF:

0.161

Gnomad AMR

AF:

0.261

Gnomad ASJ

AF:

0.308

Gnomad EAS

AF:

0.304

Gnomad SAS

AF:

0.449

Gnomad FIN

AF:

0.244

Gnomad MID

AF:

0.245

Gnomad NFE

AF:

0.231

Gnomad OTH

AF:

0.263

GnomAD3 exomes

AF:

0.281

AC:

68733

AN:

244886

Hom.:

10652

AF XY:

0.286

AC XY:

37964

AN XY:

132568

show subpopulations

Gnomad AFR exome

AF:

0.475

Gnomad AMR exome

AF:

0.233

Gnomad ASJ exome

AF:

0.289

Gnomad EAS exome

AF:

0.298

Gnomad SAS exome

AF:

0.439

Gnomad FIN exome

AF:

0.251

Gnomad NFE exome

AF:

0.232

Gnomad OTH exome

AF:

0.245

GnomAD4 exome

AF:

0.255

AC:

370192

AN:

1452116

Hom.:

50442

Cov.:

AF XY:

0.260

AC XY:

187667

AN XY:

722122

show subpopulations

Gnomad4 AFR exome

AF:

0.477

Gnomad4 AMR exome

AF:

0.233

Gnomad4 ASJ exome

AF:

0.298

Gnomad4 EAS exome

AF:

0.322

Gnomad4 SAS exome

AF:

0.436

Gnomad4 FIN exome

AF:

0.249

Gnomad4 NFE exome

AF:

0.232

Gnomad4 OTH exome

AF:

0.266

GnomAD4 genome

AF:

0.312

AC:

47422

AN:

151966

Hom.:

8382

Cov.:

AF XY:

0.314

AC XY:

23295

AN XY:

74270

show subpopulations

Gnomad4 AFR

AF:

0.472

Gnomad4 AMR

AF:

0.261

Gnomad4 ASJ

AF:

0.308

Gnomad4 EAS

AF:

0.304

Gnomad4 SAS

AF:

0.449

Gnomad4 FIN

AF:

0.244

Gnomad4 NFE

AF:

0.231

Gnomad4 OTH

AF:

0.271

Alfa

AF:

0.249

Hom.:

12568

Bravo

AF:

0.311

TwinsUK

AF:

0.236

AC:

875

ALSPAC

AF:

0.248

AC:

957

ESP6500AA

AF:

0.455

AC:

1966

ESP6500EA

AF:

0.230

AC:

1972

ExAC

AF:

0.288

AC:

34860

Asia WGS

AF:

0.411

AC:

1426

AN:

3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.056

BayesDel_addAF

Benign

-0.70

BayesDel_noAF

Benign

-0.64

CADD

Benign

5.8

DANN

Benign

0.13

DEOGEN2

Benign

0.0062

.;T

Eigen

Benign

-1.4

Eigen_PC

Benign

-1.2

FATHMM_MKL

Benign

0.16

LIST_S2

Benign

0.35

T;T

MetaRNN

Benign

0.00064

T;T

MetaSVM

Benign

-0.95

MutationAssessor

Benign

-1.6

.;N

MutationTaster

Benign

1.0

P;P;P;P

PrimateAI

Benign

0.31

PROVEAN

Benign

0.54

N;N

REVEL

Benign

0.095

Sift

Benign

1.0

T;T

Sift4G

Benign

1.0

T;T

Polyphen

0.0

B;B

Vest4

0.027

MPC

0.018

ClinPred

0.0041

GERP RS

-0.72

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.7

Varity_R

0.021

gMVP

0.054

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