rs3130100

Variant summary

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

The NM_005453.5(ZBTB22):ā€‹c.928A>Gā€‹(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 (ā˜…). Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.

Frequency

Genomes: š‘“ 0.54 ( 22195 hom., cov: 30)
Exomes š‘“: 0.53 ( 208597 hom. )

Consequence

ZBTB22
NM_005453.5 missense

Scores

18

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]

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
ZBTB22NM_005453.5 linkuse as main transcriptc.928A>G p.Thr310Ala missense_variant 2/2 ENST00000431845.3
ZBTB22NM_001145338.2 linkuse as main transcriptc.928A>G p.Thr310Ala missense_variant 2/2

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
ZBTB22ENST00000431845.3 linkuse as main transcriptc.928A>G p.Thr310Ala missense_variant 2/21 NM_005453.5 P1
ZBTB22ENST00000418724.1 linkuse as main transcriptc.928A>G p.Thr310Ala missense_variant 2/21 P1

Frequencies

GnomAD3 genomes
AF:
0.539
AC:
81662
AN:
151640
Hom.:
22160
Cov.:
30
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.:
84
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.:
30
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 submitterclinical testingLaboratory for Molecular Medicine, Mass General Brigham Personalized MedicineMar 28, 2016Variant 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
T
BayesDel_noAF
Benign
-0.80
CADD
Benign
12
DANN
Benign
0.58
DEOGEN2
Benign
0.0035
T;T
Eigen
Benign
-1.4
Eigen_PC
Benign
-1.2
FATHMM_MKL
Benign
0.12
N
LIST_S2
Benign
0.13
T;.
MetaRNN
Benign
0.000013
T;T
MetaSVM
Benign
-0.93
T
MutationAssessor
Benign
-1.4
N;N
MutationTaster
Benign
1.0
P;P
PrimateAI
Benign
0.46
T
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
T
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.

Other links and lift over

dbSNP: rs3130100; hg19: chr6-33283766; COSMIC: COSV56467442; COSMIC: COSV56467442; API