rs61753093
Variant names:
Your query was ambiguous. Multiple possible variants found:
Variant summary
Our verdict is Benign. Variant got -17 ACMG points: 0P and 17B. BP4_StrongBP6_Very_StrongBP7BS2
The NM_152743.4(BRAT1):c.2208G>T(p.Leu736Leu) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00255 in 1,613,090 control chromosomes in the GnomAD database, including 14 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Genomes: 𝑓 0.0018 ( 1 hom., cov: 34)
Exomes 𝑓: 0.0026 ( 13 hom. )
Consequence
BRAT1
NM_152743.4 synonymous
NM_152743.4 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.431
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]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -17 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.8).
BP6
Variant 7-2538327-C-A is Benign according to our data. Variant chr7-2538327-C-A is described in ClinVar as [Likely_benign]. Clinvar id is 472963.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BP7
Synonymous conserved (PhyloP=-0.431 with no splicing effect.
BS2
High Homozygotes in GnomAdExome4 at 13 AR gene
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
BRAT1 | ENST00000340611.9 | c.2208G>T | p.Leu736Leu | synonymous_variant | Exon 14 of 14 | 1 | NM_152743.4 | ENSP00000339637.4 | ||
BRAT1 | ENST00000467558.5 | n.3994G>T | non_coding_transcript_exon_variant | Exon 10 of 10 | 5 | |||||
BRAT1 | ENST00000469750.5 | n.4780G>T | non_coding_transcript_exon_variant | Exon 11 of 11 | 2 | |||||
BRAT1 | ENST00000493232.5 | n.4914G>T | non_coding_transcript_exon_variant | Exon 3 of 3 | 2 |
Frequencies
GnomAD3 genomes AF: 0.00184 AC: 280AN: 152216Hom.: 1 Cov.: 34
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GnomAD3 exomes AF: 0.00259 AC: 644AN: 248466Hom.: 3 AF XY: 0.00287 AC XY: 387AN XY: 134886
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GnomAD4 exome AF: 0.00262 AC: 3826AN: 1460756Hom.: 13 Cov.: 66 AF XY: 0.00273 AC XY: 1986AN XY: 726700
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GnomAD4 genome AF: 0.00184 AC: 281AN: 152334Hom.: 1 Cov.: 34 AF XY: 0.00203 AC XY: 151AN XY: 74506
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ClinVar
Significance: Benign/Likely benign
Submissions summary: Benign:8
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not provided Benign:6
Likely benign, criteria provided, single submitter | not provided | Breakthrough Genomics, Breakthrough Genomics | - | - - |
Likely benign, no assertion criteria provided | clinical testing | Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center | - | - - |
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Jul 01, 2024 | BRAT1: BP4, BP7, BS2 - |
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Oct 08, 2020 | - - |
Likely benign, no assertion criteria provided | clinical testing | Genome Diagnostics Laboratory, University Medical Center Utrecht | - | - - |
Benign, criteria provided, single submitter | clinical testing | Athena Diagnostics | Jun 07, 2019 | - - |
BRAT1-related disorder Benign:1
Likely benign, no assertion criteria provided | clinical testing | PreventionGenetics, part of Exact Sciences | Oct 24, 2019 | This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Neonatal-onset encephalopathy with rigidity and seizures Benign:1
Benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Jan 30, 2025 | - - |
Computational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at