rs966762013

Variant names:

Your query was ambiguous. Multiple possible variants found:

Variant summary

Our verdict is Likely benign. The variant received -5 ACMG points: 2P and 7B. PM2BP4_StrongBP6_ModerateBP7

The NM_152743.4(BRAT1):c.114G>C(p.Thr38Thr) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000558 in 1,613,568 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★). Synonymous variant affecting the same amino acid position (i.e. T38T) has been classified as Likely benign.

Frequency

Genomes: 𝑓 0.000033 ( 0 hom., cov: 33)

Exomes 𝑓: 0.0000027 ( 0 hom. )

Consequence

BRAT1
NM_152743.4 synonymous

Scores

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: -4.80

Publications

0 publications found

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 Gene-Disease associations (from GenCC):

neonatal-onset encephalopathy with rigidity and seizures
Inheritance: AR Classification: DEFINITIVE, STRONG, SUPPORTIVE Submitted by: Ambry Genetics, Orphanet, ClinGen, G2P, Labcorp Genetics (formerly Invitae)
neurodevelopmental disorder with cerebellar atrophy and with or without seizures
Inheritance: AR Classification: DEFINITIVE Submitted by: ClinGen, Ambry Genetics

BRAT1 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Likely_benign. The variant received -5 ACMG points.

PM2

Very rare variant in population databases, with high coverage;

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.89).

BP6

Variant 7-2554318-C-G is Benign according to our data. Variant chr7-2554318-C-G is described in CliVar as Likely_benign. Clinvar id is 472931.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr7-2554318-C-G is described in CliVar as Likely_benign. Clinvar id is 472931.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr7-2554318-C-G is described in CliVar as Likely_benign. Clinvar id is 472931.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr7-2554318-C-G is described in CliVar as Likely_benign. Clinvar id is 472931.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr7-2554318-C-G is described in CliVar as Likely_benign. Clinvar id is 472931.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr7-2554318-C-G is described in CliVar as Likely_benign. Clinvar id is 472931.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr7-2554318-C-G is described in CliVar as Likely_benign. Clinvar id is 472931.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr7-2554318-C-G is described in CliVar as Likely_benign. Clinvar id is 472931.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr7-2554318-C-G is described in CliVar as Likely_benign. Clinvar id is 472931.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr7-2554318-C-G is described in CliVar as Likely_benign. Clinvar id is 472931.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr7-2554318-C-G is described in CliVar as Likely_benign. Clinvar id is 472931.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr7-2554318-C-G is described in CliVar as Likely_benign. Clinvar id is 472931.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr7-2554318-C-G is described in CliVar as Likely_benign. Clinvar id is 472931.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr7-2554318-C-G is described in CliVar as Likely_benign. Clinvar id is 472931.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr7-2554318-C-G is described in CliVar as Likely_benign. Clinvar id is 472931.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr7-2554318-C-G is described in CliVar as Likely_benign. Clinvar id is 472931.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr7-2554318-C-G is described in CliVar as Likely_benign. Clinvar id is 472931.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr7-2554318-C-G is described in CliVar as Likely_benign. Clinvar id is 472931.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr7-2554318-C-G is described in CliVar as Likely_benign. Clinvar id is 472931.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr7-2554318-C-G is described in CliVar as Likely_benign. Clinvar id is 472931.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr7-2554318-C-G is described in CliVar as Likely_benign. Clinvar id is 472931.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr7-2554318-C-G is described in CliVar as Likely_benign. Clinvar id is 472931.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr7-2554318-C-G is described in CliVar as Likely_benign. Clinvar id is 472931.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr7-2554318-C-G is described in CliVar as Likely_benign. Clinvar id is 472931.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr7-2554318-C-G is described in CliVar as Likely_benign. Clinvar id is 472931.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr7-2554318-C-G is described in CliVar as Likely_benign. Clinvar id is 472931.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr7-2554318-C-G is described in CliVar as Likely_benign. Clinvar id is 472931.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr7-2554318-C-G is described in CliVar as Likely_benign. Clinvar id is 472931.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr7-2554318-C-G is described in CliVar as Likely_benign. Clinvar id is 472931.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr7-2554318-C-G is described in CliVar as Likely_benign. Clinvar id is 472931.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr7-2554318-C-G is described in CliVar as Likely_benign. Clinvar id is 472931.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr7-2554318-C-G is described in CliVar as Likely_benign. Clinvar id is 472931.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr7-2554318-C-G is described in CliVar as Likely_benign. Clinvar id is 472931.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr7-2554318-C-G is described in CliVar as Likely_benign. Clinvar id is 472931.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr7-2554318-C-G is described in CliVar as Likely_benign. Clinvar id is 472931.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr7-2554318-C-G is described in CliVar as Likely_benign. Clinvar id is 472931.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr7-2554318-C-G is described in CliVar as Likely_benign. Clinvar id is 472931.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr7-2554318-C-G is described in CliVar as Likely_benign. Clinvar id is 472931.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr7-2554318-C-G is described in CliVar as Likely_benign. Clinvar id is 472931.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr7-2554318-C-G is described in CliVar as Likely_benign. Clinvar id is 472931.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr7-2554318-C-G is described in CliVar as Likely_benign. Clinvar id is 472931.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr7-2554318-C-G is described in CliVar as Likely_benign. Clinvar id is 472931.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr7-2554318-C-G is described in CliVar as Likely_benign. Clinvar id is 472931.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr7-2554318-C-G is described in CliVar as Likely_benign. Clinvar id is 472931.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr7-2554318-C-G is described in CliVar as Likely_benign. Clinvar id is 472931.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr7-2554318-C-G is described in CliVar as Likely_benign. Clinvar id is 472931.Status of the report is criteria_provided_single_submitter, 1 stars.

BP7

Synonymous conserved (PhyloP=-4.8 with no splicing effect.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
BRAT1	NM_152743.4 link	c.114G>C	p.Thr38Thr	synonymous_variant	Exon 2 of 14	ENST00000340611.9	NP_689956.2	Q6PJG6-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	UniProt
BRAT1	ENST00000340611.9 link	c.114G>C	p.Thr38Thr	synonymous_variant	Exon 2 of 14	1	NM_152743.4	ENSP00000339637.4	Q6PJG6-1
BRAT1	ENST00000421712.1 link	n.114G>C		non_coding_transcript_exon_variant	Exon 1 of 5	3		ENSP00000409209.2	F8WDN5
BRAT1	ENST00000467558.5 link	n.130G>C		non_coding_transcript_exon_variant	Exon 1 of 10	5
BRAT1	ENST00000469750.5 link	n.338G>C		non_coding_transcript_exon_variant	Exon 2 of 11	2

Frequencies

GnomAD3 genomes

AF:

0.0000328

AC:

AN:

152234

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0000241

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.000262

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.00

Gnomad OTH

AF:

0.00

GnomAD2 exomes

AF:

0.00000796

AC:

AN:

251352

AF XY:

0.00000736

show subpopulations

Gnomad AFR exome

AF:

0.00

Gnomad AMR exome

AF:

0.0000579

Gnomad ASJ exome

AF:

0.00

Gnomad EAS exome

AF:

0.00

Gnomad FIN exome

AF:

0.00

Gnomad NFE exome

AF:

0.00

Gnomad OTH exome

AF:

0.00

GnomAD4 exome

AF:

0.00000274

AC:

AN:

1461334

Hom.:

Cov.:

AF XY:

0.00000138

AC XY:

AN XY:

726994

show subpopulations

African (AFR)

AF:

0.00

AC:

AN:

33474

American (AMR)

AF:

0.0000447

AC:

AN:

44704

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

26116

East Asian (EAS)

AF:

0.00

AC:

AN:

39684

South Asian (SAS)

AF:

0.00

AC:

AN:

86172

European-Finnish (FIN)

AF:

0.00

AC:

AN:

53352

Middle Eastern (MID)

AF:

0.00

AC:

AN:

5766

European-Non Finnish (NFE)

AF:

0.00

AC:

AN:

1111710

Other (OTH)

AF:

0.0000331

AC:

AN:

60356

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.438

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

AF:

0.0000328

AC:

AN:

152234

Hom.:

Cov.:

AF XY:

0.0000269

AC XY:

AN XY:

74378

show subpopulations

African (AFR)

AF:

0.0000241

AC:

AN:

41458

American (AMR)

AF:

0.000262

AC:

AN:

15288

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

3472

East Asian (EAS)

AF:

0.00

AC:

AN:

5204

South Asian (SAS)

AF:

0.00

AC:

AN:

4830

European-Finnish (FIN)

AF:

0.00

AC:

AN:

10626

Middle Eastern (MID)

AF:

0.00

AC:

AN:

316

European-Non Finnish (NFE)

AF:

0.00

AC:

AN:

68038

Other (OTH)

AF:

0.00

AC:

AN:

2090

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.545

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Variant carriers

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.00

Hom.:

Bravo

AF:

0.0000453

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

Neonatal-onset encephalopathy with rigidity and seizures

Benign:1

Jan 20, 2025

Labcorp Genetics (formerly Invitae), Labcorp

Significance:Likely 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

-0.89

CADD

Benign

0.20

(source)

DANN

Benign

0.63

PhyloP100

-4.8

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

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

Other links and lift over