Variant chr5-138179811-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP4_StrongBP6_Very_StrongBS2

The NM_005733.3(KIF20A):c.131C>T(p.Ser44Phe) variant causes a missense change. The variant allele was found at a frequency of 0.0037 in 1,614,062 control chromosomes in the GnomAD database, including 20 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).

Frequency

Genomes: 𝑓 0.0029 ( 3 hom., cov: 32)

Exomes 𝑓: 0.0038 ( 17 hom. )

Consequence

KIF20A
NM_005733.3 missense

Scores

Clinical Significance

Likely benign criteria provided, multiple submitters, no conflicts B:3

Conservation

PhyloP100: 5.81

Variant links:

Genes affected

KIF20A (HGNC:9787): (kinesin family member 20A) Enables protein kinase binding activity. Involved in microtubule bundle formation; midbody abscission; and regulation of cytokinesis. Located in several cellular components, including cleavage furrow; intercellular bridge; and midbody. Implicated in restrictive cardiomyopathy. [provided by Alliance of Genome Resources, Apr 2022]

KIF20A links:

KIF20A (HGNC:):

KIF20A links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -16 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.0081786215).

BP6

Variant 5-138179811-C-T is Benign according to our data. Variant chr5-138179811-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 776591.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr5-138179811-C-T is described in Lovd as [Likely_benign].

BS2

High Homozygotes in GnomAd4 at 3 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
KIF20A	NM_005733.3 linkuse as main transcript	c.131C>T	p.Ser44Phe	missense_variant	2/19	ENST00000394894.8	NP_005724.1	O95235-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
KIF20A	ENST00000394894.8 linkuse as main transcript	c.131C>T	p.Ser44Phe	missense_variant	2/19	1	NM_005733.3	ENSP00000378356.3		O95235-1

Frequencies

GnomAD3 genomes

AF:

0.00285

AC:

434

AN:

152076

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.000749

Gnomad AMI

AF:

0.00439

Gnomad AMR

AF:

0.00360

Gnomad ASJ

AF:

0.00547

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00187

Gnomad FIN

AF:

0.0000944

Gnomad MID

AF:

0.00316

Gnomad NFE

AF:

0.00451

Gnomad OTH

AF:

0.00334

GnomAD3 exomes

AF:

0.00288

AC:

724

AN:

251336

Hom.:

AF XY:

0.00278

AC XY:

377

AN XY:

135836

show subpopulations

Gnomad AFR exome

AF:

0.000554

Gnomad AMR exome

AF:

0.00333

Gnomad ASJ exome

AF:

0.00566

Gnomad EAS exome

AF:

0.0000544

Gnomad SAS exome

AF:

0.00105

Gnomad FIN exome

AF:

0.000185

Gnomad NFE exome

AF:

0.00419

Gnomad OTH exome

AF:

0.00489

GnomAD4 exome

AF:

0.00379

AC:

5535

AN:

1461868

Hom.:

Cov.:

AF XY:

0.00374

AC XY:

2723

AN XY:

727234

show subpopulations

Gnomad4 AFR exome

AF:

0.000568

Gnomad4 AMR exome

AF:

0.00344

Gnomad4 ASJ exome

AF:

0.00677

Gnomad4 EAS exome

AF:

0.0000504

Gnomad4 SAS exome

AF:

0.00108

Gnomad4 FIN exome

AF:

0.000225

Gnomad4 NFE exome

AF:

0.00434

Gnomad4 OTH exome

AF:

0.00384

GnomAD4 genome

AF:

0.00285

AC:

434

AN:

152194

Hom.:

Cov.:

AF XY:

0.00269

AC XY:

200

AN XY:

74412

show subpopulations

Gnomad4 AFR

AF:

0.000746

Gnomad4 AMR

AF:

0.00360

Gnomad4 ASJ

AF:

0.00547

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00187

Gnomad4 FIN

AF:

0.0000944

Gnomad4 NFE

AF:

0.00451

Gnomad4 OTH

AF:

0.00331

Alfa

AF:

0.00399

Hom.:

Bravo

AF:

0.00314

TwinsUK

AF:

0.00351

AC:

ALSPAC

AF:

0.00519

AC:

ESP6500AA

AF:

0.00

AC:

ESP6500EA

AF:

0.00523

AC:

ExAC

AF:

0.00288

AC:

350

Asia WGS

AF:

0.00173

AC:

AN:

3478

EpiCase

AF:

0.00523

EpiControl

AF:

0.00658

ClinVar

Significance: Likely benign

Submissions summary: Benign:3

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:3

Likely benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Likely benign, criteria provided, single submitter	clinical testing	CeGaT Center for Human Genetics Tuebingen	Mar 01, 2024	KIF20A: PP2, BP4, BS2 -
Likely benign, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Jan 31, 2024	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.17

BayesDel_addAF

Benign

-0.28

BayesDel_noAF

Benign

-0.18

CADD

Pathogenic

DANN

Uncertain

1.0

DEOGEN2

Benign

0.21

T;T;.;T

Eigen

Uncertain

0.51

Eigen_PC

Uncertain

0.51

FATHMM_MKL

Uncertain

0.91

LIST_S2

Benign

0.85

D;D;D;D

M_CAP

Uncertain

0.12

MetaRNN

Benign

0.0082

T;T;T;T

MetaSVM

Uncertain

-0.26

MutationAssessor

Uncertain

2.0

.;M;M;.

PrimateAI

Benign

0.42

PROVEAN

Uncertain

-3.5

D;D;D;D

REVEL

Benign

0.27

Sift

Uncertain

0.0010

D;D;D;D

Sift4G

Uncertain

0.010

D;T;D;D

Polyphen

1.0

.;D;.;.

Vest4

0.43, 0.43

MVP

0.85

MPC

2.4

ClinPred

0.028

GERP RS

4.6

Varity_R

0.47

gMVP

0.67

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

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over