Variant 7-73442800-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -9 ACMG points: 1P and 10B. PP2BP4_StrongBP6_ModerateBS2

The NM_032408.4(BAZ1B):c.4019G>A(p.Arg1340Lys) variant causes a missense change. The variant allele was found at a frequency of 0.00409 in 1,614,066 control chromosomes in the GnomAD database, including 14 homozygotes. In-silico tool predicts a benign outcome for this variant. 12/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.0032 ( 0 hom., cov: 32)

Exomes 𝑓: 0.0042 ( 14 hom. )

Consequence

BAZ1B
NM_032408.4 missense

Scores

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: 4.24

Variant links:

Genes affected

BAZ1B (HGNC:961): (bromodomain adjacent to zinc finger domain 1B) This gene encodes a member of the bromodomain protein family. The bromodomain is a structural motif characteristic of proteins involved in chromatin-dependent regulation of transcription. This gene is deleted in Williams-Beuren syndrome, a developmental disorder caused by deletion of multiple genes at 7q11.23. [provided by RefSeq, Jul 2008]

BAZ1B links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -9 ACMG points.

PP2

Missense variant where missense usually causes diseases, BAZ1B

BP4

Computational evidence support a benign effect (MetaRNN=0.008951694).

BP6

Variant 7-73442800-C-T is Benign according to our data. Variant chr7-73442800-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 715404.Status of the report is criteria_provided_single_submitter, 1 stars.

BS2

High AC in GnomAd4 at 491 AD gene.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
BAZ1B	NM_032408.4 linkuse as main transcript	c.4019G>A	p.Arg1340Lys	missense_variant	18/20	ENST00000339594.9
BAZ1B	NM_001370402.1 linkuse as main transcript	c.4019G>A	p.Arg1340Lys	missense_variant	18/19

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
BAZ1B	ENST00000339594.9 linkuse as main transcript	c.4019G>A	p.Arg1340Lys	missense_variant	18/20	1	NM_032408.4	P1	Q9UIG0-1
BAZ1B	ENST00000404251.1 linkuse as main transcript	c.4019G>A	p.Arg1340Lys	missense_variant	18/19	2		P1	Q9UIG0-1

Frequencies

GnomAD3 genomes

AF:

0.00323

AC:

492

AN:

152220

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00121

Gnomad AMI

AF:

0.00219

Gnomad AMR

AF:

0.00268

Gnomad ASJ

AF:

0.00605

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00

Gnomad FIN

AF:

0.000282

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.00545

Gnomad OTH

AF:

0.00191

GnomAD3 exomes

AF:

0.00295

AC:

742

AN:

251352

Hom.:

AF XY:

0.00306

AC XY:

416

AN XY:

135870

show subpopulations

Gnomad AFR exome

AF:

0.000615

Gnomad AMR exome

AF:

0.00168

Gnomad ASJ exome

AF:

0.00506

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.0000653

Gnomad FIN exome

AF:

0.000277

Gnomad NFE exome

AF:

0.00526

Gnomad OTH exome

AF:

0.00277

GnomAD4 exome

AF:

0.00418

AC:

6115

AN:

1461728

Hom.:

Cov.:

AF XY:

0.00422

AC XY:

3068

AN XY:

727144

show subpopulations

Gnomad4 AFR exome

AF:

0.000508

Gnomad4 AMR exome

AF:

0.00181

Gnomad4 ASJ exome

AF:

0.00528

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.0000927

Gnomad4 FIN exome

AF:

0.000412

Gnomad4 NFE exome

AF:

0.00505

Gnomad4 OTH exome

AF:

0.00356

GnomAD4 genome

AF:

0.00322

AC:

491

AN:

152338

Hom.:

Cov.:

AF XY:

0.00311

AC XY:

232

AN XY:

74488

show subpopulations

Gnomad4 AFR

AF:

0.00120

Gnomad4 AMR

AF:

0.00262

Gnomad4 ASJ

AF:

0.00605

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00

Gnomad4 FIN

AF:

0.000282

Gnomad4 NFE

AF:

0.00545

Gnomad4 OTH

AF:

0.00189

Alfa

AF:

0.00521

Hom.:

Bravo

AF:

0.00333

TwinsUK

AF:

0.00378

AC:

ALSPAC

AF:

0.00597

AC:

ESP6500AA

AF:

0.000454

AC:

ESP6500EA

AF:

0.00605

AC:

ExAC

AF:

0.00268

AC:

326

Asia WGS

AF:

0.000289

AC:

AN:

3478

EpiCase

AF:

0.00491

EpiControl

AF:

0.00533

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Likely benign, criteria provided, single submitter

clinical testing

Invitae

Dec 31, 2019

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.15

BayesDel_addAF

Benign

-0.47

BayesDel_noAF

Benign

-0.44

CADD

Benign

DANN

Uncertain

0.99

DEOGEN2

Benign

0.10

T;T

Eigen

Benign

0.026

Eigen_PC

Uncertain

0.24

FATHMM_MKL

Uncertain

0.95

M_CAP

Benign

0.012

MetaRNN

Benign

0.0090

T;T

MetaSVM

Benign

-1.1

MutationAssessor

Benign

0.90

L;L

MutationTaster

Benign

0.99

D;D

PrimateAI

Uncertain

0.65

PROVEAN

Benign

-0.44

N;N

REVEL

Benign

0.093

Sift

Benign

0.12

T;T

Sift4G

Benign

0.69

T;T

Polyphen

0.21

B;B

Vest4

0.35

MVP

0.35

MPC

0.22

ClinPred

0.024

GERP RS

5.9

Varity_R

0.17

gMVP

0.41

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