X-40051808-A-ATT

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_Moderate BA1

The NM_001123385.2(BCOR):c.*300_*301insAA variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.19 (1610 hom., 5127 hem., cov: 18)
  • Exomes 𝑓: 0.13 (584 hom. 2257 hem.)
• Consequence: BCOR NM_001123385.2 3_prime_UTR
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.603

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]

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP6: Variant X-40051808-A-ATT is Benign according to our data. Variant chrX-40051808-A-ATT is described in ClinVar as [Benign]. Clinvar id is 1228197.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.212 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
BCOR	NM_001123385.2	c.*300_*301insAA		3_prime_UTR_variant	15/15	ENST00000378444.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
BCOR	ENST00000378444.9	c.*300_*301insAA		3_prime_UTR_variant	15/15	1	NM_001123385.2	P2

Frequencies

GnomAD3 genomes AF: 0.187 AC: 20429 AN: 109144 Hom.: 1612 Cov.: 18 AF XY: 0.161 AC XY: 5127 AN XY: 31748

Gnomad AFR AF: 0.216

Gnomad AMI AF: 0.418

Gnomad AMR AF: 0.140

Gnomad ASJ AF: 0.180

Gnomad EAS AF: 0.000562

Gnomad SAS AF: 0.170

Gnomad FIN AF: 0.0887

Gnomad MID AF: 0.203

Gnomad NFE AF: 0.202

Gnomad OTH AF: 0.171

GnomAD4 exome AF: 0.133 AC: 15148 AN: 113882 Hom.: 584 Cov.: 0 AF XY: 0.0825 AC XY: 2257 AN XY: 27344

Gnomad4 AFR exome AF: 0.173

Gnomad4 AMR exome AF: 0.0903

Gnomad4 ASJ exome AF: 0.134

Gnomad4 EAS exome AF: 0.0000838

Gnomad4 SAS exome AF: 0.106

Gnomad4 FIN exome AF: 0.0868

Gnomad4 NFE exome AF: 0.158

Gnomad4 OTH exome AF: 0.149

GnomAD4 genome AF: 0.187 AC: 20417 AN: 109186 Hom.: 1610 Cov.: 18 AF XY: 0.161 AC XY: 5127 AN XY: 31804

Gnomad4 AFR AF: 0.216

Gnomad4 AMR AF: 0.140

Gnomad4 ASJ AF: 0.180

Gnomad4 EAS AF: 0.000564

Gnomad4 SAS AF: 0.169

Gnomad4 FIN AF: 0.0887

Gnomad4 NFE AF: 0.202

Gnomad4 OTH AF: 0.168

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Aug 31, 2019

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Computational scores

Source: dbNSFP v4.3

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs35289701; hg19: chrX-39911061;