Variant 1-155015779-C-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.1119C>A(p.Pro373Pro) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0121 in 1,612,224 control chromosomes in the GnomAD database, including 201 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.011 ( 27 hom., cov: 33)

Exomes 𝑓: 0.012 ( 174 hom. )

Consequence

ZBTB7B
NM_001256455.2 synonymous

Scores

Clinical Significance

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

Conservation

PhyloP100: -0.0500

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:

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=-0.49).

BP6

Variant 1-155015779-C-A is Benign according to our data. Variant chr1-155015779-C-A is described in ClinVar as [Benign]. Clinvar id is 713771.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BP7

Synonymous conserved (PhyloP=-0.05 with no splicing effect.

BS2

High AC in GnomAd4 at 1645 AD gene.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ZBTB7B	NM_001256455.2 linkuse as main transcript	c.1119C>A	p.Pro373Pro	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.1119C>A	p.Pro373Pro	synonymous_variant	2/3	5	NM_001256455.2	ENSP00000438647.1	O15156-1
ZBTB7B	ENST00000292176.2 linkuse as main transcript	c.1119C>A	p.Pro373Pro	synonymous_variant	1/2	1		ENSP00000292176.2	O15156-1
ZBTB7B	ENST00000368426.3 linkuse as main transcript	c.1119C>A	p.Pro373Pro	synonymous_variant	3/4	1		ENSP00000357411.3	O15156-1
ZBTB7B	ENST00000417934.6 linkuse as main transcript	c.1221C>A	p.Pro407Pro	synonymous_variant	4/5	2		ENSP00000406286.2	O15156-2

Frequencies

GnomAD3 genomes

AF:

0.0108

AC:

1646

AN:

152236

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00256

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00680

Gnomad ASJ

AF:

0.00202

Gnomad EAS

AF:

0.000193

Gnomad SAS

AF:

0.00290

Gnomad FIN

AF:

0.0521

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.0124

Gnomad OTH

AF:

0.00955

GnomAD3 exomes

AF:

0.0107

AC:

2681

AN:

249400

Hom.:

AF XY:

0.0106

AC XY:

1434

AN XY:

135304

show subpopulations

Gnomad AFR exome

AF:

0.00172

Gnomad AMR exome

AF:

0.00374

Gnomad ASJ exome

AF:

0.00419

Gnomad EAS exome

AF:

0.0000551

Gnomad SAS exome

AF:

0.00252

Gnomad FIN exome

AF:

0.0473

Gnomad NFE exome

AF:

0.0117

Gnomad OTH exome

AF:

0.0102

GnomAD4 exome

AF:

0.0123

AC:

17921

AN:

1459870

Hom.:

174

Cov.:

AF XY:

0.0118

AC XY:

8599

AN XY:

726248

show subpopulations

Gnomad4 AFR exome

AF:

0.00183

Gnomad4 AMR exome

AF:

0.00367

Gnomad4 ASJ exome

AF:

0.00394

Gnomad4 EAS exome

AF:

0.0000504

Gnomad4 SAS exome

AF:

0.00217

Gnomad4 FIN exome

AF:

0.0461

Gnomad4 NFE exome

AF:

0.0130

Gnomad4 OTH exome

AF:

0.00879

GnomAD4 genome

AF:

0.0108

AC:

1645

AN:

152354

Hom.:

Cov.:

AF XY:

0.0123

AC XY:

918

AN XY:

74506

show subpopulations

Gnomad4 AFR

AF:

0.00255

Gnomad4 AMR

AF:

0.00679

Gnomad4 ASJ

AF:

0.00202

Gnomad4 EAS

AF:

0.000193

Gnomad4 SAS

AF:

0.00269

Gnomad4 FIN

AF:

0.0521

Gnomad4 NFE

AF:

0.0124

Gnomad4 OTH

AF:

0.00945

Alfa

AF:

0.0111

Hom.:

Bravo

AF:

0.00694

Asia WGS

AF:

0.000289

AC:

AN:

3478

EpiCase

AF:

0.00872

EpiControl

AF:

0.00984

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	Jul 02, 2018	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.49

CADD

Benign

9.4

DANN

Benign

0.83

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