Variant 17-7462072-G-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -17 ACMG points: 0P and 17B. BP4_StrongBP6_Very_StrongBP7BS2

The ENST00000380599.9(ZBTB4):c.2910C>T(p.Tyr970=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00686 in 1,599,964 control chromosomes in the GnomAD database, including 47 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.0052 ( 7 hom., cov: 33)

Exomes 𝑓: 0.0070 ( 40 hom. )

Consequence

ZBTB4
ENST00000380599.9 synonymous

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: 0.605

Variant links:

Genes affected

ZBTB4 (HGNC:23847): (zinc finger and BTB domain containing 4) Enables several functions, including DNA-binding transcription repressor activity, RNA polymerase II-specific; methyl-CpNpG binding activity; and sequence-specific DNA binding activity. Involved in cellular response to DNA damage stimulus and negative regulation of transcription by RNA polymerase II. Located in cytosol and nuclear body. [provided by Alliance of Genome Resources, Apr 2022]

ZBTB4 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -17 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.66).

BP6

Variant 17-7462072-G-A is Benign according to our data. Variant chr17-7462072-G-A is described in ClinVar as [Benign]. Clinvar id is 773312.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BP7

Synonymous conserved (PhyloP=0.605 with no splicing effect.

BS2

High AC in GnomAd4 at 789 AD gene.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ZBTB4	NM_001128833.2 linkuse as main transcript	c.2910C>T	p.Tyr970=	synonymous_variant	4/4	ENST00000380599.9	NP_001122305.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ZBTB4	ENST00000380599.9 linkuse as main transcript	c.2910C>T	p.Tyr970=	synonymous_variant	4/4	1	NM_001128833.2	ENSP00000369973	P1
ZBTB4	ENST00000311403.4 linkuse as main transcript	c.2910C>T	p.Tyr970=	synonymous_variant	4/4	1		ENSP00000307858	P1

Frequencies

GnomAD3 genomes

AF:

0.00520

AC:

791

AN:

152074

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00145

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00321

Gnomad ASJ

AF:

0.00634

Gnomad EAS

AF:

0.000192

Gnomad SAS

AF:

0.000622

Gnomad FIN

AF:

0.00490

Gnomad MID

AF:

0.0127

Gnomad NFE

AF:

0.00865

Gnomad OTH

AF:

0.00575

GnomAD3 exomes

AF:

0.00548

AC:

1299

AN:

237138

Hom.:

AF XY:

0.00556

AC XY:

710

AN XY:

127760

show subpopulations

Gnomad AFR exome

AF:

0.00168

Gnomad AMR exome

AF:

0.00236

Gnomad ASJ exome

AF:

0.00833

Gnomad EAS exome

AF:

0.000492

Gnomad SAS exome

AF:

0.000501

Gnomad FIN exome

AF:

0.00443

Gnomad NFE exome

AF:

0.00905

Gnomad OTH exome

AF:

0.00687

GnomAD4 exome

AF:

0.00703

AC:

10183

AN:

1447772

Hom.:

Cov.:

AF XY:

0.00695

AC XY:

4999

AN XY:

719182

show subpopulations

Gnomad4 AFR exome

AF:

0.00102

Gnomad4 AMR exome

AF:

0.00304

Gnomad4 ASJ exome

AF:

0.00845

Gnomad4 EAS exome

AF:

0.000177

Gnomad4 SAS exome

AF:

0.000607

Gnomad4 FIN exome

AF:

0.00461

Gnomad4 NFE exome

AF:

0.00820

Gnomad4 OTH exome

AF:

0.00653

GnomAD4 genome

AF:

0.00518

AC:

789

AN:

152192

Hom.:

Cov.:

AF XY:

0.00513

AC XY:

382

AN XY:

74412

show subpopulations

Gnomad4 AFR

AF:

0.00145

Gnomad4 AMR

AF:

0.00320

Gnomad4 ASJ

AF:

0.00634

Gnomad4 EAS

AF:

0.000193

Gnomad4 SAS

AF:

0.000622

Gnomad4 FIN

AF:

0.00490

Gnomad4 NFE

AF:

0.00864

Gnomad4 OTH

AF:

0.00569

Alfa

AF:

0.00741

Hom.:

Bravo

AF:

0.00506

Asia WGS

AF:

0.000866

AC:

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Apr 09, 2018	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.66

CADD

Benign

4.5

DANN

Benign

0.80

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