Variant 20-63790269-A-G details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP7BA1

The NM_001369741.1(ZBTB46):c.489T>C(p.Ala163Ala) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.147 in 1,611,810 control chromosomes in the GnomAD database, including 21,026 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as association (no stars).

Frequency

Genomes: 𝑓 0.18 ( 3236 hom., cov: 33)

Exomes 𝑓: 0.14 ( 17790 hom. )

Consequence

ZBTB46
NM_001369741.1 synonymous

Scores

Clinical Significance

association no assertion criteria provided O:1

Conservation

PhyloP100: -2.03

Variant links:

Genes affected

ZBTB46 (HGNC:16094): (zinc finger and BTB domain containing 46) Predicted to enable DNA-binding transcription factor activity, RNA polymerase II-specific and RNA polymerase II transcription regulatory region sequence-specific DNA binding activity. Predicted to be involved in regulation of transcription by RNA polymerase II. Predicted to act upstream of or within regulation of leukocyte differentiation. Predicted to be part of chromatin. Predicted to be active in nucleus. [provided by Alliance of Genome Resources, Apr 2022]

ZBTB46 links:

ZBTB46 (HGNC:):

ZBTB46 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -13 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.87).

BP7

Synonymous conserved (PhyloP=-2.03 with no splicing effect.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.43 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ZBTB46	NM_001369741.1 linkuse as main transcript	c.489T>C	p.Ala163Ala	synonymous_variant	2/5	ENST00000245663.9	NP_001356670.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	UniProt
ZBTB46	ENST00000245663.9 linkuse as main transcript	c.489T>C	p.Ala163Ala	synonymous_variant	2/5	5	NM_001369741.1	ENSP00000245663.3	Q86UZ6
ZBTB46	ENST00000302995.2 linkuse as main transcript	c.489T>C	p.Ala163Ala	synonymous_variant	2/7	2		ENSP00000303102.2	Q86UZ6
ZBTB46	ENST00000395104.5 linkuse as main transcript	c.489T>C	p.Ala163Ala	synonymous_variant	1/4	2		ENSP00000378536.1	Q86UZ6
ZBTB46	ENST00000650966.1 linkuse as main transcript	n.489T>C		non_coding_transcript_exon_variant	2/6			ENSP00000498245.1	A0A494BZW5

Frequencies

GnomAD3 genomes

AF:

0.183

AC:

27885

AN:

152104

Hom.:

3220

Cov.:

show subpopulations

Gnomad AFR

AF:

0.285

Gnomad AMI

AF:

0.181

Gnomad AMR

AF:

0.180

Gnomad ASJ

AF:

0.0642

Gnomad EAS

AF:

0.447

Gnomad SAS

AF:

0.171

Gnomad FIN

AF:

0.118

Gnomad MID

AF:

0.0764

Gnomad NFE

AF:

0.121

Gnomad OTH

AF:

0.143

GnomAD3 exomes

AF:

0.169

AC:

41719

AN:

247358

Hom.:

4637

AF XY:

0.160

AC XY:

21509

AN XY:

134062

show subpopulations

Gnomad AFR exome

AF:

0.286

Gnomad AMR exome

AF:

0.197

Gnomad ASJ exome

AF:

0.0654

Gnomad EAS exome

AF:

0.461

Gnomad SAS exome

AF:

0.162

Gnomad FIN exome

AF:

0.117

Gnomad NFE exome

AF:

0.119

Gnomad OTH exome

AF:

0.136

GnomAD4 exome

AF:

0.143

AC:

209229

AN:

1459588

Hom.:

17790

Cov.:

AF XY:

0.142

AC XY:

103261

AN XY:

726044

show subpopulations

Gnomad4 AFR exome

AF:

0.284

Gnomad4 AMR exome

AF:

0.193

Gnomad4 ASJ exome

AF:

0.0634

Gnomad4 EAS exome

AF:

0.440

Gnomad4 SAS exome

AF:

0.155

Gnomad4 FIN exome

AF:

0.123

Gnomad4 NFE exome

AF:

0.128

Gnomad4 OTH exome

AF:

0.150

GnomAD4 genome

AF:

0.184

AC:

27948

AN:

152222

Hom.:

3236

Cov.:

AF XY:

0.183

AC XY:

13648

AN XY:

74418

show subpopulations

Gnomad4 AFR

AF:

0.285

Gnomad4 AMR

AF:

0.180

Gnomad4 ASJ

AF:

0.0642

Gnomad4 EAS

AF:

0.445

Gnomad4 SAS

AF:

0.170

Gnomad4 FIN

AF:

0.118

Gnomad4 NFE

AF:

0.121

Gnomad4 OTH

AF:

0.147

Alfa

AF:

0.121

Hom.:

2068

Bravo

AF:

0.191

Asia WGS

AF:

0.324

AC:

1125

AN:

3478

ClinVar

Significance: association

Submissions summary: Other:1

Revision: no assertion criteria provided

LINK: link

Submissions by phenotype

Chronic osteomyelitis

Other:1

association, no assertion criteria provided

case-control

Department of Orthopeadics and Traumatology, Nanfang Hospital

Sep 01, 2016

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.87

CADD

Benign

0.19

DANN

Benign

0.23

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