rs190344757
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Variant summary
Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_StrongBP6_ModerateBP7BS2
The NM_001123385.2(BCOR):c.3036C>T(p.Pro1012=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000051 in 1,195,064 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 15 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.000062 ( 0 hom., 3 hem., cov: 23)
Exomes 𝑓: 0.000050 ( 0 hom. 12 hem. )
Consequence
BCOR
NM_001123385.2 synonymous
NM_001123385.2 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 3.25
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 -11 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.52).
BP6
?
Variant X-40071652-G-A is Benign according to our data. Variant chrX-40071652-G-A is described in ClinVar as [Benign]. Clinvar id is 465157.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
Synonymous conserved (PhyloP=3.24 with no splicing effect.
BS2
?
High Hemizygotes in GnomAd4 at 3 XL gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
BCOR | NM_001123385.2 | c.3036C>T | p.Pro1012= | synonymous_variant | 5/15 | ENST00000378444.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
BCOR | ENST00000378444.9 | c.3036C>T | p.Pro1012= | synonymous_variant | 5/15 | 1 | NM_001123385.2 | P2 |
Frequencies
GnomAD3 genomes ? AF: 0.0000624 AC: 7AN: 112107Hom.: 0 Cov.: 23 AF XY: 0.0000875 AC XY: 3AN XY: 34303
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GnomAD3 exomes AF: 0.0000877 AC: 16AN: 182397Hom.: 0 AF XY: 0.0000897 AC XY: 6AN XY: 66919
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GnomAD4 exome AF: 0.0000499 AC: 54AN: 1082905Hom.: 0 Cov.: 25 AF XY: 0.0000343 AC XY: 12AN XY: 350335
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GnomAD4 genome ? AF: 0.0000624 AC: 7AN: 112159Hom.: 0 Cov.: 23 AF XY: 0.0000873 AC XY: 3AN XY: 34365
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
Oculofaciocardiodental syndrome Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Aug 07, 2021 | - - |
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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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at