7-2538147-T-C
Variant summary
Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1
The NM_152743.4(BRAT1):c.2388A>G(p.Glu796=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.363 in 1,607,532 control chromosomes in the GnomAD database, including 111,247 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Genomes: 𝑓 0.45 ( 17030 hom., cov: 34)
Exomes 𝑓: 0.35 ( 94217 hom. )
Consequence
BRAT1
NM_152743.4 synonymous
NM_152743.4 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.444
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 -21 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.77).
BP6
?
Variant 7-2538147-T-C is Benign according to our data. Variant chr7-2538147-T-C is described in ClinVar as [Benign]. Clinvar id is 585490.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr7-2538147-T-C is described in Lovd as [Benign].
BP7
?
Synonymous conserved (PhyloP=-0.444 with no splicing effect.
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.664 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
BRAT1 | NM_152743.4 | c.2388A>G | p.Glu796= | synonymous_variant | 14/14 | ENST00000340611.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
BRAT1 | ENST00000340611.9 | c.2388A>G | p.Glu796= | synonymous_variant | 14/14 | 1 | NM_152743.4 | P1 | |
BRAT1 | ENST00000467558.5 | n.4174A>G | non_coding_transcript_exon_variant | 10/10 | 5 | ||||
BRAT1 | ENST00000469750.5 | n.4960A>G | non_coding_transcript_exon_variant | 11/11 | 2 | ||||
BRAT1 | ENST00000493232.5 | n.5094A>G | non_coding_transcript_exon_variant | 3/3 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.449 AC: 68279AN: 152070Hom.: 16997 Cov.: 34
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GnomAD3 exomes AF: 0.387 AC: 93845AN: 242584Hom.: 19148 AF XY: 0.377 AC XY: 50046AN XY: 132762
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GnomAD4 exome AF: 0.354 AC: 514874AN: 1455344Hom.: 94217 Cov.: 54 AF XY: 0.351 AC XY: 254034AN XY: 722856
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GnomAD4 genome ? AF: 0.449 AC: 68366AN: 152188Hom.: 17030 Cov.: 34 AF XY: 0.451 AC XY: 33547AN XY: 74404
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ClinVar
Significance: Benign
Submissions summary: Benign:5
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not specified Benign:2
Benign, no assertion criteria provided | clinical testing | Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen | - | - - |
Benign, no assertion criteria provided | clinical testing | Joint Genome Diagnostic Labs from Nijmegen and Maastricht, Radboudumc and MUMC+ | - | - - |
not provided Benign:2
Benign, criteria provided, single submitter | clinical testing | GeneDx | Jul 07, 2018 | - - |
Benign, criteria provided, single submitter | clinical testing | Athena Diagnostics | Apr 20, 2017 | - - |
Neonatal-onset encephalopathy with rigidity and seizures Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Feb 01, 2024 | - - |
Computational scores
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BayesDel_noAF
Benign
Cadd
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Dann
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at