Variant chr1-155015230-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 NM_001256455.2(ZBTB7B):c.570G>A(p.Pro190Pro) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00502 in 1,613,434 control chromosomes in the GnomAD database, including 42 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).

Frequency

Genomes: 𝑓 0.0045 ( 4 hom., cov: 33)

Exomes 𝑓: 0.0051 ( 38 hom. )

Consequence

ZBTB7B
NM_001256455.2 synonymous

Scores

Clinical Significance

Benign/Likely benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: -2.73

Variant links:

Genes affected

ZBTB7B (HGNC:18668): (zinc finger and BTB domain containing 7B) This gene encodes a zinc finger-containing transcription factor that acts as a key regulator of lineage commitment of immature T-cell precursors. It is necessary and sufficient for commitment of CD4 lineage, while its absence causes CD8 commitment. It also functions as a transcriptional repressor of type I collagen genes. Alternatively spliced transcript variants have been found for this gene. [provided by RefSeq, Jan 2012]

ZBTB7B links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -17 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.86).

BP6

Variant 1-155015230-G-A is Benign according to our data. Variant chr1-155015230-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 710306.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BP7

Synonymous conserved (PhyloP=-2.73 with no splicing effect.

BS2

High AC in GnomAd4 at 678 AD gene.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ZBTB7B	NM_001256455.2 linkuse as main transcript	c.570G>A	p.Pro190Pro	synonymous_variant	2/3	ENST00000535420.6	NP_001243384.1	O15156-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	UniProt
ZBTB7B	ENST00000535420.6 linkuse as main transcript	c.570G>A	p.Pro190Pro	synonymous_variant	2/3	5	NM_001256455.2	ENSP00000438647.1	O15156-1
ZBTB7B	ENST00000292176.2 linkuse as main transcript	c.570G>A	p.Pro190Pro	synonymous_variant	1/2	1		ENSP00000292176.2	O15156-1
ZBTB7B	ENST00000368426.3 linkuse as main transcript	c.570G>A	p.Pro190Pro	synonymous_variant	3/4	1		ENSP00000357411.3	O15156-1
ZBTB7B	ENST00000417934.6 linkuse as main transcript	c.672G>A	p.Pro224Pro	synonymous_variant	4/5	2		ENSP00000406286.2	O15156-2

Frequencies

GnomAD3 genomes

AF:

0.00446

AC:

678

AN:

151996

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.000918

Gnomad AMI

AF:

0.0164

Gnomad AMR

AF:

0.00472

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.000193

Gnomad SAS

AF:

0.00228

Gnomad FIN

AF:

0.0168

Gnomad MID

AF:

0.00949

Gnomad NFE

AF:

0.00519

Gnomad OTH

AF:

0.00335

GnomAD3 exomes

AF:

0.00467

AC:

1160

AN:

248384

Hom.:

AF XY:

0.00477

AC XY:

644

AN XY:

134952

show subpopulations

Gnomad AFR exome

AF:

0.000702

Gnomad AMR exome

AF:

0.00214

Gnomad ASJ exome

AF:

0.000200

Gnomad EAS exome

AF:

0.0000547

Gnomad SAS exome

AF:

0.00432

Gnomad FIN exome

AF:

0.0139

Gnomad NFE exome

AF:

0.00549

Gnomad OTH exome

AF:

0.00443

GnomAD4 exome

AF:

0.00508

AC:

7417

AN:

1461320

Hom.:

Cov.:

AF XY:

0.00507

AC XY:

3689

AN XY:

726940

show subpopulations

Gnomad4 AFR exome

AF:

0.000627

Gnomad4 AMR exome

AF:

0.00179

Gnomad4 ASJ exome

AF:

0.0000765

Gnomad4 EAS exome

AF:

0.0000756

Gnomad4 SAS exome

AF:

0.00383

Gnomad4 FIN exome

AF:

0.0159

Gnomad4 NFE exome

AF:

0.00529

Gnomad4 OTH exome

AF:

0.00392

GnomAD4 genome

AF:

0.00446

AC:

678

AN:

152114

Hom.:

Cov.:

AF XY:

0.00481

AC XY:

358

AN XY:

74378

show subpopulations

Gnomad4 AFR

AF:

0.000915

Gnomad4 AMR

AF:

0.00471

Gnomad4 ASJ

AF:

0.00

Gnomad4 EAS

AF:

0.000193

Gnomad4 SAS

AF:

0.00228

Gnomad4 FIN

AF:

0.0168

Gnomad4 NFE

AF:

0.00519

Gnomad4 OTH

AF:

0.00332

Alfa

AF:

0.00442

Hom.:

Bravo

AF:

0.00308

Asia WGS

AF:

0.00289

AC:

AN:

3478

EpiCase

AF:

0.00453

EpiControl

AF:

0.00450

ClinVar

Significance: Benign/Likely benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Likely benign, criteria provided, single submitter	clinical testing	CeGaT Center for Human Genetics Tuebingen	Jan 01, 2023	ZBTB7B: BP4, BP7, BS2 -
Benign, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Jul 02, 2018	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.86

CADD

Benign

1.6

DANN

Benign

0.88

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