rs61753095

Variant names:

Variant summary

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

The NM_152743.4(BRAT1):c.699G>A(p.Thr233Thr) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.193 in 1,569,366 control chromosomes in the GnomAD database, including 31,752 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.15 ( 2278 hom., cov: 32)

Exomes 𝑓: 0.20 ( 29474 hom. )

Consequence

BRAT1
NM_152743.4 synonymous

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:4

Conservation

PhyloP100: -3.22

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=-0.77).

BP6

Variant 7-2543694-C-T is Benign according to our data. Variant chr7-2543694-C-T is described in ClinVar as [Benign]. Clinvar id is 585492.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BP7

Synonymous conserved (PhyloP=-3.22 with no splicing effect.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.205 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
BRAT1	NM_152743.4 link	c.699G>A	p.Thr233Thr	synonymous_variant	Exon 5 of 14	ENST00000340611.9	NP_689956.2	Q6PJG6-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
BRAT1	ENST00000340611.9 link	c.699G>A	p.Thr233Thr	synonymous_variant	Exon 5 of 14	1	NM_152743.4	ENSP00000339637.4		Q6PJG6-1

Frequencies

GnomAD3 genomes

AF:

0.152

AC:

23120

AN:

152116

Hom.:

2270

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0414

Gnomad AMI

AF:

0.140

Gnomad AMR

AF:

0.190

Gnomad ASJ

AF:

0.148

Gnomad EAS

AF:

0.00366

Gnomad SAS

AF:

0.156

Gnomad FIN

AF:

0.248

Gnomad MID

AF:

0.104

Gnomad NFE

AF:

0.207

Gnomad OTH

AF:

0.151

GnomAD3 exomes

AF:

0.175

AC:

39580

AN:

226326

Hom.:

4200

AF XY:

0.177

AC XY:

21563

AN XY:

121888

show subpopulations

Gnomad AFR exome

AF:

0.0362

Gnomad AMR exome

AF:

0.205

Gnomad ASJ exome

AF:

0.155

Gnomad EAS exome

AF:

0.00231

Gnomad SAS exome

AF:

0.154

Gnomad FIN exome

AF:

0.242

Gnomad NFE exome

AF:

0.210

Gnomad OTH exome

AF:

0.189

GnomAD4 exome

AF:

0.197

AC:

279673

AN:

1417132

Hom.:

29474

Cov.:

AF XY:

0.196

AC XY:

136937

AN XY:

698142

show subpopulations

Gnomad4 AFR exome

AF:

0.0342

Gnomad4 AMR exome

AF:

0.205

Gnomad4 ASJ exome

AF:

0.154

Gnomad4 EAS exome

AF:

0.00136

Gnomad4 SAS exome

AF:

0.160

Gnomad4 FIN exome

AF:

0.244

Gnomad4 NFE exome

AF:

0.212

Gnomad4 OTH exome

AF:

0.178

GnomAD4 genome

AF:

0.152

AC:

23141

AN:

152234

Hom.:

2278

Cov.:

AF XY:

0.152

AC XY:

11324

AN XY:

74432

show subpopulations

Gnomad4 AFR

AF:

0.0416

Gnomad4 AMR

AF:

0.191

Gnomad4 ASJ

AF:

0.148

Gnomad4 EAS

AF:

0.00347

Gnomad4 SAS

AF:

0.154

Gnomad4 FIN

AF:

0.248

Gnomad4 NFE

AF:

0.208

Gnomad4 OTH

AF:

0.151

Alfa

AF:

0.177

Hom.:

1068

Bravo

AF:

0.142

Asia WGS

AF:

0.0810

AC:

279

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:4

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Apr 20, 2017

Athena Diagnostics

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Jul 27, 2018

GeneDx

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

not specified

Benign:1

Jul 15, 2024

Unidad de Genómica Garrahan, Hospital de Pediatría Garrahan

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

This variant is classified as Benign based on local population frequency. This variant was detected in 41% of patients studied in a panel designed for Epileptic and Developmental Encephalopathy and Progressive Myoclonus Epilepsy. Number of patients: 38. Only high quality variants are reported. -

Neonatal-onset encephalopathy with rigidity and seizures

Benign:1

Feb 04, 2025

Labcorp Genetics (formerly Invitae), Labcorp

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.77

CADD

Benign

0.22

DANN

Benign

0.72

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.7

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.010

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