rs192133446
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Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 2P and 12B. PM2BP4_StrongBP6_Very_Strong
The NM_152743.4(BRAT1):c.282+9G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000164 in 1,613,902 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Genomes: 𝑓 0.00092 ( 0 hom., cov: 32)
Exomes 𝑓: 0.000086 ( 1 hom. )
Consequence
BRAT1
NM_152743.4 intron
NM_152743.4 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: -1.32
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 -10 ACMG points.
PM2
?
Very rare variant in population databases, with high coverage;
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.8).
BP6
?
Variant 7-2547315-C-T is Benign according to our data. Variant chr7-2547315-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 472966.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
BRAT1 | NM_152743.4 | c.282+9G>A | intron_variant | ENST00000340611.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
BRAT1 | ENST00000340611.9 | c.282+9G>A | intron_variant | 1 | NM_152743.4 | P1 | |||
BRAT1 | ENST00000421712.1 | c.282+9G>A | intron_variant, NMD_transcript_variant | 3 | |||||
BRAT1 | ENST00000467558.5 | n.298+9G>A | intron_variant, non_coding_transcript_variant | 5 | |||||
BRAT1 | ENST00000469750.5 | n.506+9G>A | intron_variant, non_coding_transcript_variant | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.000913 AC: 139AN: 152192Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.000275 AC: 69AN: 250680Hom.: 1 AF XY: 0.000199 AC XY: 27AN XY: 135690
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GnomAD4 exome AF: 0.0000855 AC: 125AN: 1461592Hom.: 1 Cov.: 30 AF XY: 0.0000784 AC XY: 57AN XY: 727062
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GnomAD4 genome ? AF: 0.000919 AC: 140AN: 152310Hom.: 0 Cov.: 32 AF XY: 0.000953 AC XY: 71AN XY: 74470
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ClinVar
Significance: Benign/Likely benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
BRAT1-related disorder Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Feb 17, 2020 | 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 | Invitae | Jan 29, 2024 | - - |
Computational scores
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Name
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
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