6-151365770-C-T

Variant summary

Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_ModerateBP6_ModerateBP7BA1

The NM_020861.3(ZBTB2):​c.1296G>A​(p.Glu432Glu) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.597 in 1,613,910 control chromosomes in the GnomAD database, including 295,435 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.54 ( 23512 hom., cov: 32)
Exomes 𝑓: 0.60 ( 271923 hom. )

Consequence

ZBTB2
NM_020861.3 synonymous

Scores

2

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.458
Variant links:
Genes affected
ZBTB2 (HGNC:20868): (zinc finger and BTB domain containing 2) Enables DNA-binding transcription repressor activity, RNA polymerase II-specific; RNA polymerase II cis-regulatory region sequence-specific DNA binding activity; and identical protein binding activity. Involved in negative regulation of transcription by RNA polymerase II. Predicted to be active in nucleoplasm. [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 -13 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.44).
BP6
Variant 6-151365770-C-T is Benign according to our data. Variant chr6-151365770-C-T is described in ClinVar as [Benign]. Clinvar id is 1286394.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
Synonymous conserved (PhyloP=0.458 with no splicing effect.
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.632 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
ZBTB2NM_020861.3 linkc.1296G>A p.Glu432Glu synonymous_variant Exon 3 of 3 ENST00000325144.5 NP_065912.1 Q8N680

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
ZBTB2ENST00000325144.5 linkc.1296G>A p.Glu432Glu synonymous_variant Exon 3 of 3 1 NM_020861.3 ENSP00000323183.4 Q8N680

Frequencies

GnomAD3 genomes
AF:
0.541
AC:
82180
AN:
151934
Hom.:
23510
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.391
Gnomad AMI
AF:
0.421
Gnomad AMR
AF:
0.557
Gnomad ASJ
AF:
0.589
Gnomad EAS
AF:
0.294
Gnomad SAS
AF:
0.378
Gnomad FIN
AF:
0.677
Gnomad MID
AF:
0.440
Gnomad NFE
AF:
0.637
Gnomad OTH
AF:
0.539
GnomAD3 exomes
AF:
0.554
AC:
139177
AN:
251332
Hom.:
40667
AF XY:
0.549
AC XY:
74589
AN XY:
135840
show subpopulations
Gnomad AFR exome
AF:
0.390
Gnomad AMR exome
AF:
0.583
Gnomad ASJ exome
AF:
0.591
Gnomad EAS exome
AF:
0.280
Gnomad SAS exome
AF:
0.384
Gnomad FIN exome
AF:
0.675
Gnomad NFE exome
AF:
0.630
Gnomad OTH exome
AF:
0.580
GnomAD4 exome
AF:
0.603
AC:
881746
AN:
1461858
Hom.:
271923
Cov.:
80
AF XY:
0.597
AC XY:
434157
AN XY:
727224
show subpopulations
Gnomad4 AFR exome
AF:
0.380
Gnomad4 AMR exome
AF:
0.578
Gnomad4 ASJ exome
AF:
0.591
Gnomad4 EAS exome
AF:
0.354
Gnomad4 SAS exome
AF:
0.383
Gnomad4 FIN exome
AF:
0.669
Gnomad4 NFE exome
AF:
0.637
Gnomad4 OTH exome
AF:
0.567
GnomAD4 genome
AF:
0.541
AC:
82216
AN:
152052
Hom.:
23512
Cov.:
32
AF XY:
0.538
AC XY:
39991
AN XY:
74314
show subpopulations
Gnomad4 AFR
AF:
0.391
Gnomad4 AMR
AF:
0.557
Gnomad4 ASJ
AF:
0.589
Gnomad4 EAS
AF:
0.295
Gnomad4 SAS
AF:
0.379
Gnomad4 FIN
AF:
0.677
Gnomad4 NFE
AF:
0.637
Gnomad4 OTH
AF:
0.533
Alfa
AF:
0.606
Hom.:
64159
Bravo
AF:
0.528
Asia WGS
AF:
0.338
AC:
1180
AN:
3478
EpiCase
AF:
0.622
EpiControl
AF:
0.625

ClinVar

Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

not provided Benign:1
Jan 15, 2020
GeneDx
Significance: Benign
Review Status: criteria provided, single submitter
Collection Method: clinical testing

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Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.44
CADD
Benign
8.7
DANN
Benign
0.50

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: rs11155787; hg19: chr6-151686905; COSMIC: COSV57312030; API