7-2538108-C-G
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Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 2P and 7B. PM2BP4_StrongBP6_ModerateBP7
The NM_152743.4(BRAT1):āc.2427G>Cā(p.Thr809=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000101 in 1,591,204 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 (ā ).
Frequency
Genomes: š 0.000013 ( 0 hom., cov: 33)
Exomes š: 0.0000097 ( 0 hom. )
Consequence
BRAT1
NM_152743.4 synonymous
NM_152743.4 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -1.97
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 Likely_benign. Variant got -5 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.86).
BP6
Variant 7-2538108-C-G is Benign according to our data. Variant chr7-2538108-C-G is described in ClinVar as [Likely_benign]. Clinvar id is 1134839.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
Synonymous conserved (PhyloP=-1.97 with no splicing effect.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
BRAT1 | NM_152743.4 | c.2427G>C | p.Thr809= | synonymous_variant | 14/14 | ENST00000340611.9 | NP_689956.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
BRAT1 | ENST00000340611.9 | c.2427G>C | p.Thr809= | synonymous_variant | 14/14 | 1 | NM_152743.4 | ENSP00000339637 | P1 | |
BRAT1 | ENST00000467558.5 | n.4213G>C | non_coding_transcript_exon_variant | 10/10 | 5 | |||||
BRAT1 | ENST00000469750.5 | n.4999G>C | non_coding_transcript_exon_variant | 11/11 | 2 | |||||
BRAT1 | ENST00000493232.5 | n.5133G>C | non_coding_transcript_exon_variant | 3/3 | 2 |
Frequencies
GnomAD3 genomes AF: 0.0000131 AC: 2AN: 152228Hom.: 0 Cov.: 33
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GnomAD3 exomes AF: 0.0000169 AC: 4AN: 236864Hom.: 0 AF XY: 0.0000154 AC XY: 2AN XY: 129864
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GnomAD4 exome AF: 0.00000973 AC: 14AN: 1438976Hom.: 0 Cov.: 31 AF XY: 0.00000843 AC XY: 6AN XY: 711754
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GnomAD4 genome AF: 0.0000131 AC: 2AN: 152228Hom.: 0 Cov.: 33 AF XY: 0.00 AC XY: 0AN XY: 74376
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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
Likely benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Sep 25, 2023 | - - |
Computational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at