Variant rs62282002 details in Genebe, Genetics Data Aggregator

Variant summary

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

The NM_001376113.1(ZBTB38):c.898C>G(p.Pro300Ala) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0973 in 1,614,158 control chromosomes in the GnomAD database, including 9,479 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/20 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.085 ( 895 hom., cov: 32)

Exomes 𝑓: 0.099 ( 8584 hom. )

Consequence

ZBTB38
NM_001376113.1 missense

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.71

Variant links:

Genes affected

ZBTB38 (HGNC:26636): (zinc finger and BTB domain containing 38) The protein encoded by this gene is a zinc finger transcriptional activator that binds methylated DNA. The encoded protein can form homodimers or heterodimers through the zinc finger domains. In mouse, inhibition of this protein has been associated with apoptosis in some cell types. [provided by RefSeq, Jun 2010]

ZBTB38 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=0.0018695891).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.235 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ZBTB38	NM_001376113.1 linkuse as main transcript	c.898C>G	p.Pro300Ala	missense_variant	6/6	ENST00000321464.7	NP_001363042.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ZBTB38	ENST00000321464.7 linkuse as main transcript	c.898C>G	p.Pro300Ala	missense_variant	6/6		NM_001376113.1	ENSP00000372635	P1

Frequencies

GnomAD3 genomes

AF:

0.0852

AC:

12960

AN:

152156

Hom.:

898

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0173

Gnomad AMI

AF:

0.0570

Gnomad AMR

AF:

0.190

Gnomad ASJ

AF:

0.0873

Gnomad EAS

AF:

0.246

Gnomad SAS

AF:

0.112

Gnomad FIN

AF:

0.0992

Gnomad MID

AF:

0.104

Gnomad NFE

AF:

0.0867

Gnomad OTH

AF:

0.0874

GnomAD3 exomes

AF:

0.121

AC:

30080

AN:

249372

Hom.:

2502

AF XY:

0.117

AC XY:

15795

AN XY:

135322

show subpopulations

Gnomad AFR exome

AF:

0.0160

Gnomad AMR exome

AF:

0.237

Gnomad ASJ exome

AF:

0.0810

Gnomad EAS exome

AF:

0.256

Gnomad SAS exome

AF:

0.112

Gnomad FIN exome

AF:

0.0864

Gnomad NFE exome

AF:

0.0912

Gnomad OTH exome

AF:

0.100

GnomAD4 exome

AF:

0.0985

AC:

144042

AN:

1461884

Hom.:

8584

Cov.:

AF XY:

0.0981

AC XY:

71354

AN XY:

727240

show subpopulations

Gnomad4 AFR exome

AF:

0.0144

Gnomad4 AMR exome

AF:

0.232

Gnomad4 ASJ exome

AF:

0.0812

Gnomad4 EAS exome

AF:

0.276

Gnomad4 SAS exome

AF:

0.114

Gnomad4 FIN exome

AF:

0.0845

Gnomad4 NFE exome

AF:

0.0897

Gnomad4 OTH exome

AF:

0.0910

GnomAD4 genome

AF:

0.0850

AC:

12943

AN:

152274

Hom.:

895

Cov.:

AF XY:

0.0899

AC XY:

6690

AN XY:

74450

show subpopulations

Gnomad4 AFR

AF:

0.0173

Gnomad4 AMR

AF:

0.190

Gnomad4 ASJ

AF:

0.0873

Gnomad4 EAS

AF:

0.246

Gnomad4 SAS

AF:

0.112

Gnomad4 FIN

AF:

0.0992

Gnomad4 NFE

AF:

0.0866

Gnomad4 OTH

AF:

0.0865

Alfa

AF:

0.0815

Hom.:

466

Bravo

AF:

0.0880

TwinsUK

AF:

0.0850

AC:

315

ALSPAC

AF:

0.0942

AC:

363

ESP6500AA

AF:

0.0195

AC:

ESP6500EA

AF:

0.0887

AC:

730

ExAC

AF:

0.115

AC:

13902

Asia WGS

AF:

0.125

AC:

432

AN:

3478

EpiCase

AF:

0.0832

EpiControl

AF:

0.0804

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.081

BayesDel_addAF

Benign

-0.66

BayesDel_noAF

Benign

-0.58

CADD

Benign

DANN

Benign

0.44

DEOGEN2

Benign

0.011

T;.;T;T;T;T

Eigen

Benign

-0.21

Eigen_PC

Benign

-0.054

FATHMM_MKL

Uncertain

0.86

LIST_S2

Benign

0.58

T;T;.;.;.;T

MetaRNN

Benign

0.0019

T;T;T;T;T;T

MetaSVM

Benign

-0.91

MutationAssessor

Uncertain

2.3

.;.;M;M;M;M

MutationTaster

Benign

1.0

P;P;P

PrimateAI

Benign

0.33

PROVEAN

Benign

-0.24

.;N;N;.;N;.

REVEL

Benign

0.047

Sift

Benign

0.27

.;T;T;.;T;.

Sift4G

Benign

0.63

.;T;T;.;T;T

Polyphen

0.10

.;.;B;B;B;B

Vest4

0.088, 0.079, 0.072

MPC

0.45

ClinPred

0.013

GERP RS

5.3

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.7

Varity_R

0.027

gMVP

0.22

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