dbSNP rs1062465: KIF20B:p.Asp1011Glu (chr10-89737874-T-A) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The NM_001284259.2(KIF20B):c.3033T>A(p.Asp1011Glu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.261 in 1,612,820 control chromosomes in the GnomAD database, including 59,085 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 the same amino acid substitution has been previously reported as Likely benign in UniProt.

Frequency

Genomes: 𝑓 0.31 ( 8164 hom., cov: 32)

Exomes 𝑓: 0.26 ( 50921 hom. )

Consequence

KIF20B
NM_001284259.2 missense

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0550

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=5.992353E-4).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.456 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
KIF20B	NM_001284259.2 link	c.3033T>A	p.Asp1011Glu	missense_variant	Exon 20 of 33	ENST00000371728.8	NP_001271188.1	Q96Q89-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	UniProt
KIF20B	ENST00000371728.8 link	c.3033T>A	p.Asp1011Glu	missense_variant	Exon 20 of 33	1	NM_001284259.2	ENSP00000360793.3	Q96Q89-1
KIF20B	ENST00000260753.8 link	c.2913T>A	p.Asp971Glu	missense_variant	Exon 20 of 33	1		ENSP00000260753.4	Q96Q89-3
KIF20B	ENST00000478929.1 link	n.1579T>A		non_coding_transcript_exon_variant	Exon 7 of 20	1

Frequencies

GnomAD3 genomes

AF:

0.309

AC:

46894

AN:

151788

Hom.:

8139

Cov.:

show subpopulations

Gnomad AFR

AF:

0.462

Gnomad AMI

AF:

0.161

Gnomad AMR

AF:

0.260

Gnomad ASJ

AF:

0.308

Gnomad EAS

AF:

0.305

Gnomad SAS

AF:

0.448

Gnomad FIN

AF:

0.245

Gnomad MID

AF:

0.244

Gnomad NFE

AF:

0.231

Gnomad OTH

AF:

0.262

GnomAD3 exomes

AF:

0.282

AC:

70760

AN:

250574

Hom.:

11002

AF XY:

0.289

AC XY:

39110

AN XY:

135542

show subpopulations

Gnomad AFR exome

AF:

0.465

Gnomad AMR exome

AF:

0.235

Gnomad ASJ exome

AF:

0.290

Gnomad EAS exome

AF:

0.299

Gnomad SAS exome

AF:

0.442

Gnomad FIN exome

AF:

0.251

Gnomad NFE exome

AF:

0.232

Gnomad OTH exome

AF:

0.246

GnomAD4 exome

AF:

0.256

AC:

373786

AN:

1460914

Hom.:

50921

Cov.:

AF XY:

0.261

AC XY:

189604

AN XY:

726810

show subpopulations

Gnomad4 AFR exome

AF:

0.469

Gnomad4 AMR exome

AF:

0.235

Gnomad4 ASJ exome

AF:

0.299

Gnomad4 EAS exome

AF:

0.322

Gnomad4 SAS exome

AF:

0.437

Gnomad4 FIN exome

AF:

0.249

Gnomad4 NFE exome

AF:

0.233

Gnomad4 OTH exome

AF:

0.267

GnomAD4 genome

AF:

0.309

AC:

46950

AN:

151906

Hom.:

8164

Cov.:

AF XY:

0.311

AC XY:

23117

AN XY:

74250

show subpopulations

Gnomad4 AFR

AF:

0.462

Gnomad4 AMR

AF:

0.260

Gnomad4 ASJ

AF:

0.308

Gnomad4 EAS

AF:

0.305

Gnomad4 SAS

AF:

0.449

Gnomad4 FIN

AF:

0.245

Gnomad4 NFE

AF:

0.231

Gnomad4 OTH

AF:

0.271

Alfa

AF:

0.251

Hom.:

3948

Bravo

AF:

0.309

TwinsUK

AF:

0.236

AC:

876

ALSPAC

AF:

0.248

AC:

956

ESP6500AA

AF:

0.460

AC:

2027

ESP6500EA

AF:

0.233

AC:

2005

ExAC

AF:

0.287

AC:

34896

Asia WGS

AF:

0.410

AC:

1424

AN:

3474

EpiCase

AF:

0.227

EpiControl

AF:

0.227

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.16

BayesDel_addAF

Benign

-0.61

BayesDel_noAF

Benign

-0.51

CADD

Benign

DANN

Benign

0.96

DEOGEN2

Benign

0.019

.;T

Eigen

Benign

-0.43

Eigen_PC

Benign

-0.53

FATHMM_MKL

Benign

0.086

LIST_S2

Benign

0.62

T;T

MetaRNN

Benign

0.00060

T;T

MetaSVM

Benign

-0.95

MutationAssessor

Benign

1.9

.;L

PrimateAI

Benign

0.29

PROVEAN

Benign

-0.94

N;N

REVEL

Benign

0.097

Sift

Uncertain

0.0020

D;D

Sift4G

Benign

0.22

T;T

Polyphen

0.76

P;P

Vest4

0.020

MutPred

0.17

.;Gain of disorder (P = 0.1961);

MPC

0.027

ClinPred

0.010

GERP RS

2.2

Varity_R

0.070

gMVP

0.21

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