rs369585835
Positions:
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_ModerateBP6_ModerateBS2
The NM_001123385.2(BCOR):āc.365T>Cā(p.Met122Thr) variant causes a missense change. The variant allele was found at a frequency of 0.0000149 in 1,207,604 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 7 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (ā ).
Frequency
Genomes: š 0.000081 ( 0 hom., 3 hem., cov: 22)
Exomes š: 0.0000082 ( 0 hom. 4 hem. )
Consequence
BCOR
NM_001123385.2 missense
NM_001123385.2 missense
Scores
3
4
8
Clinical Significance
Conservation
PhyloP100: 7.14
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 -8 ACMG points.
BP4
?
Computational evidence support a benign effect (MetaRNN=0.21966705).
BP6
?
Variant X-40074981-A-G is Benign according to our data. Variant chrX-40074981-A-G is described in ClinVar as [Likely_benign]. Clinvar id is 133689.Status of the report is criteria_provided_single_submitter, 1 stars.
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.365T>C | p.Met122Thr | missense_variant | 4/15 | ENST00000378444.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
BCOR | ENST00000378444.9 | c.365T>C | p.Met122Thr | missense_variant | 4/15 | 1 | NM_001123385.2 | P2 |
Frequencies
GnomAD3 genomes ? AF: 0.0000812 AC: 9AN: 110885Hom.: 0 Cov.: 22 AF XY: 0.0000906 AC XY: 3AN XY: 33121
GnomAD3 genomes
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GnomAD3 exomes AF: 0.0000220 AC: 4AN: 181960Hom.: 0 AF XY: 0.0000301 AC XY: 2AN XY: 66528
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GnomAD4 exome AF: 0.00000821 AC: 9AN: 1096719Hom.: 0 Cov.: 34 AF XY: 0.0000110 AC XY: 4AN XY: 362359
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GnomAD4 genome ? AF: 0.0000812 AC: 9AN: 110885Hom.: 0 Cov.: 22 AF XY: 0.0000906 AC XY: 3AN XY: 33121
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1Other:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
Inborn genetic diseases Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 14, 2021 | 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. - |
not specified Other:1
not provided, no classification provided | reference population | ITMI | Sep 19, 2013 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Pathogenic
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
CADD
Benign
DANN
Uncertain
FATHMM_MKL
Pathogenic
D
M_CAP
Pathogenic
D
MetaRNN
Benign
T;T;T;T;T
MetaSVM
Benign
T
MutationAssessor
Benign
N;N;N;N;.
MutationTaster
Benign
N;N;N;N
PrimateAI
Uncertain
T
PROVEAN
Benign
N;N;N;N;N
REVEL
Benign
Sift
Uncertain
D;D;D;D;D
Sift4G
Uncertain
D;D;D;D;.
Polyphen
B;B;B;B;.
Vest4
MVP
MPC
0.31
ClinPred
T
GERP RS
RBP_binding_hub_radar
RBP_regulation_power_radar
Varity_R
gMVP
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