Variant 1-155015050-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1

The NM_001256455.2(ZBTB7B):c.390C>T(p.Ile130Ile) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.466 in 1,613,498 control chromosomes in the GnomAD database, including 184,252 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.48 ( 18609 hom., cov: 32)

Exomes 𝑓: 0.46 ( 165643 hom. )

Consequence

ZBTB7B
NM_001256455.2 synonymous

Scores

Clinical Significance

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

Conservation

PhyloP100: 1.72

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 -21 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.47).

BP6

Variant 1-155015050-C-T is Benign according to our data. Variant chr1-155015050-C-T is described in ClinVar as [Benign]. Clinvar id is 1225107.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BP7

Synonymous conserved (PhyloP=1.72 with no splicing effect.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.878 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ZBTB7B	NM_001256455.2 link	c.390C>T	p.Ile130Ile	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 link	c.390C>T	p.Ile130Ile	synonymous_variant	2/3	5	NM_001256455.2	ENSP00000438647.1	O15156-1
ZBTB7B	ENST00000292176.2 link	c.390C>T	p.Ile130Ile	synonymous_variant	1/2	1		ENSP00000292176.2	O15156-1
ZBTB7B	ENST00000368426.3 link	c.390C>T	p.Ile130Ile	synonymous_variant	3/4	1		ENSP00000357411.3	O15156-1
ZBTB7B	ENST00000417934.6 link	c.492C>T	p.Ile164Ile	synonymous_variant	4/5	2		ENSP00000406286.2	O15156-2

Frequencies

GnomAD3 genomes

AF:

0.484

AC:

73478

AN:

151816

Hom.:

18617

Cov.:

show subpopulations

Gnomad AFR

AF:

0.477

Gnomad AMI

AF:

0.326

Gnomad AMR

AF:

0.586

Gnomad ASJ

AF:

0.541

Gnomad EAS

AF:

0.900

Gnomad SAS

AF:

0.667

Gnomad FIN

AF:

0.445

Gnomad MID

AF:

0.570

Gnomad NFE

AF:

0.426

Gnomad OTH

AF:

0.478

GnomAD3 exomes

AF:

0.534

AC:

133576

AN:

250252

Hom.:

38448

AF XY:

0.531

AC XY:

71989

AN XY:

135598

show subpopulations

Gnomad AFR exome

AF:

0.470

Gnomad AMR exome

AF:

0.675

Gnomad ASJ exome

AF:

0.544

Gnomad EAS exome

AF:

0.899

Gnomad SAS exome

AF:

0.651

Gnomad FIN exome

AF:

0.448

Gnomad NFE exome

AF:

0.426

Gnomad OTH exome

AF:

0.507

GnomAD4 exome

AF:

0.464

AC:

678056

AN:

1461564

Hom.:

165643

Cov.:

AF XY:

0.470

AC XY:

341595

AN XY:

727090

show subpopulations

Gnomad4 AFR exome

AF:

0.484

Gnomad4 AMR exome

AF:

0.666

Gnomad4 ASJ exome

AF:

0.539

Gnomad4 EAS exome

AF:

0.913

Gnomad4 SAS exome

AF:

0.647

Gnomad4 FIN exome

AF:

0.454

Gnomad4 NFE exome

AF:

0.421

Gnomad4 OTH exome

AF:

0.497

GnomAD4 genome

AF:

0.484

AC:

73503

AN:

151934

Hom.:

18609

Cov.:

AF XY:

0.492

AC XY:

36563

AN XY:

74264

show subpopulations

Gnomad4 AFR

AF:

0.476

Gnomad4 AMR

AF:

0.586

Gnomad4 ASJ

AF:

0.541

Gnomad4 EAS

AF:

0.899

Gnomad4 SAS

AF:

0.665

Gnomad4 FIN

AF:

0.445

Gnomad4 NFE

AF:

0.426

Gnomad4 OTH

AF:

0.475

Alfa

AF:

0.449

Hom.:

30975

Bravo

AF:

0.493

Asia WGS

AF:

0.709

AC:

2462

AN:

3478

EpiCase

AF:

0.442

EpiControl

AF:

0.443

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	GeneDx	Nov 09, 2018	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.47

CADD

Benign

9.4

DANN

Benign

0.93

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.7

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