7-2538603-T-C

Variant summary

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

The NM_152743.4(BRAT1):c.1932A>G(p.Arg644=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.362 in 1,597,032 control chromosomes in the GnomAD database, including 109,578 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★). Synonymous variant affecting the same amino acid position (i.e. R644R) has been classified as Likely benign.

Frequency

Genomes: 𝑓 0.45 ( 16930 hom., cov: 33)

Exomes 𝑓: 0.35 ( 92648 hom. )

Consequence

BRAT1
NM_152743.4 synonymous

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:5

Conservation

PhyloP100: 0.00800

Variant links:

Genes affected

BRAT1 (HGNC:21701): (BRCA1 associated ATM activator 1) The protein encoded by this ubiquitously expressed gene interacts with the tumor suppressing BRCA1 (breast cancer 1) protein and and the ATM (ataxia telangiectasia mutated) protein. ATM is thought to be a master controller of cell cycle checkpoint signalling pathways that are required for cellular responses to DNA damage such as double-strand breaks that are induced by ionizing radiation and complexes with BRCA1 in the multi-protein complex BASC (BRAC1-associated genome surveillance complex). The protein encoded by this gene is thought to play a role in the DNA damage pathway regulated by BRCA1 and ATM. [provided by RefSeq, Mar 2012]

BRAT1 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=-0.84).

BP6

Variant 7-2538603-T-C is Benign according to our data. Variant chr7-2538603-T-C is described in ClinVar as [Benign]. Clinvar id is 585489.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr7-2538603-T-C is described in Lovd as [Benign].

BP7

Synonymous conserved (PhyloP=0.008 with no splicing effect.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.662 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
BRAT1	NM_152743.4 linkuse as main transcript	c.1932A>G	p.Arg644=	synonymous_variant	14/14	ENST00000340611.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
BRAT1	ENST00000340611.9 linkuse as main transcript	c.1932A>G	p.Arg644=	synonymous_variant	14/14	1	NM_152743.4	P1	Q6PJG6-1

Frequencies

GnomAD3 genomes

AF:

0.448

AC:

68051

AN:

151896

Hom.:

16898

Cov.:

show subpopulations

Gnomad AFR

AF:

0.668

Gnomad AMI

AF:

0.462

Gnomad AMR

AF:

0.418

Gnomad ASJ

AF:

0.286

Gnomad EAS

AF:

0.369

Gnomad SAS

AF:

0.337

Gnomad FIN

AF:

0.489

Gnomad MID

AF:

0.326

Gnomad NFE

AF:

0.338

Gnomad OTH

AF:

0.421

GnomAD3 exomes

AF:

0.385

AC:

86750

AN:

225130

Hom.:

17321

AF XY:

0.376

AC XY:

47034

AN XY:

125150

show subpopulations

Gnomad AFR exome

AF:

0.678

Gnomad AMR exome

AF:

0.430

Gnomad ASJ exome

AF:

0.299

Gnomad EAS exome

AF:

0.362

Gnomad SAS exome

AF:

0.330

Gnomad FIN exome

AF:

0.492

Gnomad NFE exome

AF:

0.348

Gnomad OTH exome

AF:

0.370

GnomAD4 exome

AF:

0.353

AC:

509491

AN:

1445018

Hom.:

92648

Cov.:

AF XY:

0.350

AC XY:

252045

AN XY:

719226

show subpopulations

Gnomad4 AFR exome

AF:

0.677

Gnomad4 AMR exome

AF:

0.430

Gnomad4 ASJ exome

AF:

0.298

Gnomad4 EAS exome

AF:

0.363

Gnomad4 SAS exome

AF:

0.331

Gnomad4 FIN exome

AF:

0.477

Gnomad4 NFE exome

AF:

0.337

Gnomad4 OTH exome

AF:

0.365

GnomAD4 genome

AF:

0.448

AC:

68137

AN:

152014

Hom.:

16930

Cov.:

AF XY:

0.450

AC XY:

33438

AN XY:

74316

show subpopulations

Gnomad4 AFR

AF:

0.668

Gnomad4 AMR

AF:

0.419

Gnomad4 ASJ

AF:

0.286

Gnomad4 EAS

AF:

0.368

Gnomad4 SAS

AF:

0.335

Gnomad4 FIN

AF:

0.489

Gnomad4 NFE

AF:

0.338

Gnomad4 OTH

AF:

0.419

Alfa

AF:

0.286

Hom.:

1169

Bravo

AF:

0.454

Asia WGS

AF:

0.352

AC:

1221

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:5

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not specified

Benign:2

Benign, no assertion criteria provided	clinical testing	Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen	-	- -
Benign, no assertion criteria provided	clinical testing	Joint Genome Diagnostic Labs from Nijmegen and Maastricht, Radboudumc and MUMC+	-	- -

not provided

Benign:2

Benign, criteria provided, single submitter	clinical testing	GeneDx	Jul 17, 2018	- -
Benign, criteria provided, single submitter	clinical testing	Athena Diagnostics	Apr 20, 2017	- -

Neonatal-onset encephalopathy with rigidity and seizures

Benign:1

Benign, criteria provided, single submitter

clinical testing

Invitae

Feb 01, 2024

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.84

Cadd

Benign

6.2

Dann

Benign

0.42

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