Variant 7-2537850-G-T details in Genebe, Genetics Data Aggregator

Variant summary

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

The NM_152743.4(BRAT1):c.*219C>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0121 in 697,314 control chromosomes in the GnomAD database, including 126 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).

Frequency

Genomes: 𝑓 0.013 ( 18 hom., cov: 33)

Exomes 𝑓: 0.012 ( 108 hom. )

Consequence

BRAT1
NM_152743.4 3_prime_UTR

Scores

Clinical Significance

Likely benign criteria provided, multiple submitters, no conflicts B:3

Conservation

PhyloP100: -0.0160

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:

BRAT1 (HGNC:):

BRAT1 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.92).

BP6

Variant 7-2537850-G-T is Benign according to our data. Variant chr7-2537850-G-T is described in ClinVar as [Likely_benign]. Clinvar id is 1186082.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAdExome4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.0574 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
BRAT1	NM_152743.4 linkuse as main transcript	c.*219C>A		3_prime_UTR_variant	14/14	ENST00000340611.9	NP_689956.2	Q6PJG6-1

Ensembl

Gene	Transcript	HGVSc	Effect	#exon/exons	TSL	MANE	Protein	UniProt
BRAT1	ENST00000340611 linkuse as main transcript	c.*219C>A	3_prime_UTR_variant	14/14	1	NM_152743.4	ENSP00000339637.4	Q6PJG6-1
BRAT1	ENST00000467558.5 linkuse as main transcript	n.*31C>A	downstream_gene_variant		5
BRAT1	ENST00000469750.5 linkuse as main transcript	n.*31C>A	downstream_gene_variant		2
BRAT1	ENST00000493232.5 linkuse as main transcript	n.*31C>A	downstream_gene_variant		2

Frequencies

GnomAD3 genomes

AF:

0.0127

AC:

1935

AN:

152214

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0197

Gnomad AMI

AF:

0.00987

Gnomad AMR

AF:

0.00857

Gnomad ASJ

AF:

0.0135

Gnomad EAS

AF:

0.0240

Gnomad SAS

AF:

0.0360

Gnomad FIN

AF:

0.00452

Gnomad MID

AF:

0.0411

Gnomad NFE

AF:

0.00794

Gnomad OTH

AF:

0.0158

GnomAD4 exome

AF:

0.0120

AC:

6520

AN:

544982

Hom.:

108

Cov.:

AF XY:

0.0121

AC XY:

3264

AN XY:

269508

show subpopulations

Gnomad4 AFR exome

AF:

0.0195

Gnomad4 AMR exome

AF:

0.00798

Gnomad4 ASJ exome

AF:

0.0146

Gnomad4 EAS exome

AF:

0.0598

Gnomad4 SAS exome

AF:

0.0321

Gnomad4 FIN exome

AF:

0.00363

Gnomad4 NFE exome

AF:

0.00813

Gnomad4 OTH exome

AF:

0.0122

GnomAD4 genome

AF:

0.0127

AC:

1936

AN:

152332

Hom.:

Cov.:

AF XY:

0.0131

AC XY:

974

AN XY:

74502

show subpopulations

Gnomad4 AFR

AF:

0.0196

Gnomad4 AMR

AF:

0.00856

Gnomad4 ASJ

AF:

0.0135

Gnomad4 EAS

AF:

0.0241

Gnomad4 SAS

AF:

0.0364

Gnomad4 FIN

AF:

0.00452

Gnomad4 NFE

AF:

0.00794

Gnomad4 OTH

AF:

0.0156

Alfa

AF:

0.0101

Hom.:

Bravo

AF:

0.0128

Asia WGS

AF:

0.0180

AC:

AN:

3478

ClinVar

Significance: Likely benign

Submissions summary: Benign:3

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Likely benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Likely benign, criteria provided, single submitter	clinical testing	GeneDx	Jul 17, 2018	- -

Neonatal-onset encephalopathy with rigidity and seizures;C4748032:Neurodevelopmental disorder with cerebellar atrophy and with or without seizures

Benign:1

Likely benign, criteria provided, single submitter

clinical testing

Fulgent Genetics, Fulgent Genetics

Aug 16, 2021

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.92

CADD

Benign

0.70

DANN

Benign

0.42

Splicing

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