rs760093247
Variant summary
Our verdict is Benign. Variant got -17 ACMG points: 0P and 17B. BP4_StrongBP6_Very_StrongBP7BS2
The NM_001123385.2(BCOR):c.4824A>C(p.Pro1608=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000174 in 1,209,200 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 8 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Genomes: 𝑓 0.0000089 ( 0 hom., 1 hem., cov: 23)
Exomes 𝑓: 0.000018 ( 0 hom. 7 hem. )
Consequence
BCOR
NM_001123385.2 synonymous
NM_001123385.2 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -1.08
Genes affected
BCOR (HGNC:20893): (BCL6 corepressor) The protein encoded by this gene was identified as an interacting corepressor of BCL6, a POZ/zinc finger transcription repressor that is required for germinal center formation and may influence apoptosis. This protein selectively interacts with the POZ domain of BCL6, but not with eight other POZ proteins. Specific class I and II histone deacetylases (HDACs) have been shown to interact with this protein, which suggests a possible link between the two classes of HDACs. Several transcript variants encoding different isoforms have been found for this gene. A pseudogene of this gene is found on chromosome Y.[provided by RefSeq, Jun 2010]
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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=-0.81).
BP6
?
Variant X-40054038-T-G is Benign according to our data. Variant chrX-40054038-T-G is described in ClinVar as [Likely_benign]. Clinvar id is 465161.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BP7
?
Synonymous conserved (PhyloP=-1.08 with no splicing effect.
BS2
?
High Hemizygotes in GnomAdExome at 5 XL gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
BCOR | NM_001123385.2 | c.4824A>C | p.Pro1608= | synonymous_variant | 14/15 | ENST00000378444.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
BCOR | ENST00000378444.9 | c.4824A>C | p.Pro1608= | synonymous_variant | 14/15 | 1 | NM_001123385.2 | P2 |
Frequencies
GnomAD3 genomes ? AF: 0.00000892 AC: 1AN: 112086Hom.: 0 Cov.: 23 AF XY: 0.0000292 AC XY: 1AN XY: 34246
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GnomAD3 exomes AF: 0.000116 AC: 21AN: 180885Hom.: 0 AF XY: 0.0000764 AC XY: 5AN XY: 65445
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GnomAD4 exome AF: 0.0000182 AC: 20AN: 1097114Hom.: 0 Cov.: 31 AF XY: 0.0000193 AC XY: 7AN XY: 362492
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GnomAD4 genome ? AF: 0.00000892 AC: 1AN: 112086Hom.: 0 Cov.: 23 AF XY: 0.0000292 AC XY: 1AN XY: 34246
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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
Inborn genetic diseases Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | May 27, 2016 | This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. - |
Oculofaciocardiodental syndrome Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Mar 06, 2021 | - - |
Computational scores
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Name
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BayesDel_noAF
Benign
Cadd
Benign
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