Genetic Variant BRAT1:c.*12G>C (chr7-2538057-C-G) – ACMG Classification: Benign (-20 pts)

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_152743.4(BRAT1):c.*12G>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.153 in 1,539,028 control chromosomes in the GnomAD database, including 20,015 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.12 ( 1520 hom., cov: 33)

Exomes 𝑓: 0.16 ( 18495 hom. )

Consequence

BRAT1
NM_152743.4 3_prime_UTR

Scores

Clinical Significance

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

Conservation

PhyloP100: -1.53

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:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.96).

BP6

Variant 7-2538057-C-G is Benign according to our data. Variant chr7-2538057-C-G is described in ClinVar as [Benign]. Clinvar id is 1253787.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.164 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
BRAT1	NM_152743.4 link	c.*12G>C		3_prime_UTR_variant	Exon 14 of 14	ENST00000340611.9	NP_689956.2	Q6PJG6-1

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL	MANE	Protein	UniProt
BRAT1	ENST00000340611 link	c.*12G>C	3_prime_UTR_variant	Exon 14 of 14	1	NM_152743.4	ENSP00000339637.4	Q6PJG6-1
BRAT1	ENST00000467558.5 link	n.4264G>C	non_coding_transcript_exon_variant	Exon 10 of 10	5
BRAT1	ENST00000469750.5 link	n.5050G>C	non_coding_transcript_exon_variant	Exon 11 of 11	2
BRAT1	ENST00000493232.5 link	n.5184G>C	non_coding_transcript_exon_variant	Exon 3 of 3	2

Frequencies

GnomAD3 genomes

AF:

0.122

AC:

18487

AN:

152104

Hom.:

1514

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0312

Gnomad AMI

AF:

0.0958

Gnomad AMR

AF:

0.167

Gnomad ASJ

AF:

0.0956

Gnomad EAS

AF:

0.00271

Gnomad SAS

AF:

0.0758

Gnomad FIN

AF:

0.211

Gnomad MID

AF:

0.0475

Gnomad NFE

AF:

0.167

Gnomad OTH

AF:

0.115

GnomAD3 exomes

AF:

0.137

AC:

26844

AN:

195372

Hom.:

2309

AF XY:

0.136

AC XY:

14390

AN XY:

105422

show subpopulations

Gnomad AFR exome

AF:

0.0259

Gnomad AMR exome

AF:

0.189

Gnomad ASJ exome

AF:

0.0925

Gnomad EAS exome

AF:

0.00193

Gnomad SAS exome

AF:

0.0748

Gnomad FIN exome

AF:

0.205

Gnomad NFE exome

AF:

0.166

Gnomad OTH exome

AF:

0.147

GnomAD4 exome

AF:

0.157

AC:

217664

AN:

1386806

Hom.:

18495

Cov.:

AF XY:

0.154

AC XY:

105007

AN XY:

679802

show subpopulations

Gnomad4 AFR exome

AF:

0.0238

Gnomad4 AMR exome

AF:

0.188

Gnomad4 ASJ exome

AF:

0.0924

Gnomad4 EAS exome

AF:

0.00121

Gnomad4 SAS exome

AF:

0.0791

Gnomad4 FIN exome

AF:

0.207

Gnomad4 NFE exome

AF:

0.171

Gnomad4 OTH exome

AF:

0.137

GnomAD4 genome

AF:

0.122

AC:

18501

AN:

152222

Hom.:

1520

Cov.:

AF XY:

0.121

AC XY:

9037

AN XY:

74396

show subpopulations

Gnomad4 AFR

AF:

0.0311

Gnomad4 AMR

AF:

0.168

Gnomad4 ASJ

AF:

0.0956

Gnomad4 EAS

AF:

0.00252

Gnomad4 SAS

AF:

0.0746

Gnomad4 FIN

AF:

0.211

Gnomad4 NFE

AF:

0.167

Gnomad4 OTH

AF:

0.115

Alfa

AF:

0.135

Hom.:

349

Bravo

AF:

0.115

Asia WGS

AF:

0.0530

AC:

182

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

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 23% of patients studied in a panel designed for Epileptic and Developmental Encephalopathy and Progressive Myoclonus Epilepsy. Number of patients: 21. Only high quality variants are reported. -

not provided

Benign:1

Jul 15, 2018

GeneDx

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

-0.96

CADD

Benign

0.072

DANN

Benign

0.27

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