Variant rs3130100 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1

The NM_005453.5(ZBTB22):c.928A>G(p.Thr310Ala) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.533 in 1,613,586 control chromosomes in the GnomAD database, including 230,792 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★). Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.

Frequency

Genomes: 𝑓 0.54 ( 22195 hom., cov: 30)

Exomes 𝑓: 0.53 ( 208597 hom. )

Consequence

ZBTB22
NM_005453.5 missense

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 1.62

Variant links:

Genes affected

ZBTB22 (HGNC:13085): (zinc finger and BTB domain containing 22) Enables sequence-specific double-stranded DNA binding activity. Predicted to be involved in regulation of transcription by RNA polymerase II. Predicted to be part of chromatin. Predicted to be active in nucleus. [provided by Alliance of Genome Resources, Apr 2022]

ZBTB22 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -14 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=1.3302328E-5).

BP6

Variant 6-33315989-T-C is Benign according to our data. Variant chr6-33315989-T-C is described in ClinVar as [Benign]. Clinvar id is 403519.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.615 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ZBTB22	NM_005453.5 linkuse as main transcript	c.928A>G	p.Thr310Ala	missense_variant	2/2	ENST00000431845.3
ZBTB22	NM_001145338.2 linkuse as main transcript	c.928A>G	p.Thr310Ala	missense_variant	2/2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ZBTB22	ENST00000431845.3 linkuse as main transcript	c.928A>G	p.Thr310Ala	missense_variant	2/2	1	NM_005453.5	P1
ZBTB22	ENST00000418724.1 linkuse as main transcript	c.928A>G	p.Thr310Ala	missense_variant	2/2	1		P1

Frequencies

GnomAD3 genomes

AF:

0.539

AC:

81662

AN:

151640

Hom.:

22160

Cov.:

show subpopulations

Gnomad AFR

AF:

0.554

Gnomad AMI

AF:

0.412

Gnomad AMR

AF:

0.557

Gnomad ASJ

AF:

0.573

Gnomad EAS

AF:

0.371

Gnomad SAS

AF:

0.634

Gnomad FIN

AF:

0.527

Gnomad MID

AF:

0.545

Gnomad NFE

AF:

0.533

Gnomad OTH

AF:

0.532

GnomAD3 exomes

AF:

0.540

AC:

135569

AN:

251230

Hom.:

37224

AF XY:

0.547

AC XY:

74276

AN XY:

135874

show subpopulations

Gnomad AFR exome

AF:

0.561

Gnomad AMR exome

AF:

0.532

Gnomad ASJ exome

AF:

0.562

Gnomad EAS exome

AF:

0.350

Gnomad SAS exome

AF:

0.643

Gnomad FIN exome

AF:

0.526

Gnomad NFE exome

AF:

0.542

Gnomad OTH exome

AF:

0.553

GnomAD4 exome

AF:

0.532

AC:

777628

AN:

1461828

Hom.:

208597

Cov.:

AF XY:

0.536

AC XY:

389921

AN XY:

727216

show subpopulations

Gnomad4 AFR exome

AF:

0.566

Gnomad4 AMR exome

AF:

0.534

Gnomad4 ASJ exome

AF:

0.567

Gnomad4 EAS exome

AF:

0.342

Gnomad4 SAS exome

AF:

0.643

Gnomad4 FIN exome

AF:

0.527

Gnomad4 NFE exome

AF:

0.528

Gnomad4 OTH exome

AF:

0.539

GnomAD4 genome

AF:

0.539

AC:

81752

AN:

151758

Hom.:

22195

Cov.:

AF XY:

0.541

AC XY:

40124

AN XY:

74138

show subpopulations

Gnomad4 AFR

AF:

0.554

Gnomad4 AMR

AF:

0.556

Gnomad4 ASJ

AF:

0.573

Gnomad4 EAS

AF:

0.370

Gnomad4 SAS

AF:

0.634

Gnomad4 FIN

AF:

0.527

Gnomad4 NFE

AF:

0.533

Gnomad4 OTH

AF:

0.531

Alfa

AF:

0.535

Hom.:

44923

Bravo

AF:

0.539

TwinsUK

AF:

0.519

AC:

1923

ALSPAC

AF:

0.522

AC:

2012

ESP6500AA

AF:

0.558

AC:

2459

ESP6500EA

AF:

0.541

AC:

4652

ExAC

AF:

0.546

AC:

66275

Asia WGS

AF:

0.500

AC:

1740

AN:

3478

EpiCase

AF:

0.541

EpiControl

AF:

0.536

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not specified

Benign:1

Benign, criteria provided, single submitter

clinical testing

Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine

Mar 28, 2016

Variant identified in a genome or exome case(s) and assessed due to predicted null impact of the variant or pathogenic assertions in the literature or databases. Disclaimer: This variant has not undergone full assessment. The following are preliminary notes: MAF -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.078

BayesDel_addAF

Benign

-0.81

BayesDel_noAF

Benign

-0.80

CADD

Benign

DANN

Benign

0.58

DEOGEN2

Benign

0.0035

T;T

Eigen

Benign

-1.4

Eigen_PC

Benign

-1.2

FATHMM_MKL

Benign

0.12

LIST_S2

Benign

0.13

T;.

MetaRNN

Benign

0.000013

T;T

MetaSVM

Benign

-0.93

MutationAssessor

Benign

-1.4

N;N

MutationTaster

Benign

1.0

P;P

PrimateAI

Benign

0.46

PROVEAN

Benign

0.25

N;N

REVEL

Benign

0.051

Sift

Benign

1.0

T;T

Sift4G

Benign

0.93

T;T

Polyphen

0.0

B;B

Vest4

0.022

MPC

0.56

ClinPred

0.0018

GERP RS

3.0

Varity_R

0.074

gMVP

0.044

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