chr12-122022128-CGG-C

Position:

• chr12-122022128-CGG-C

Variant summary

Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2

The NM_001024808.3(BCL7A):​c.39_40delGG​(p.Ala14fs) variant causes a frameshift change. The variant was absent in control chromosomes in GnomAD project. Variant has been reported in ClinVar as other (no stars).

• Frequency: Genomes: not found (cov: 29)
• Consequence: BCL7A NM_001024808.3 frameshift
• Clinical Significance: - - O:1
• Conservation: PhyloP100: 5.73

Genes affected

BCL7A (HGNC:1004): (BAF chromatin remodeling complex subunit BCL7A) This gene is directly involved, with Myc and IgH, in a three-way gene translocation in a Burkitt lymphoma cell line. As a result of the gene translocation, the N-terminal region of the gene product is disrupted, which is thought to be related to the pathogenesis of a subset of high-grade B cell non-Hodgkin lymphoma. The N-terminal segment involved in the translocation includes the region that shares a strong sequence similarity with those of BCL7B and BCL7C. Two transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jul 2008]

BCL7A (HGNC:):

ACMG classification

Verdict is Uncertain_significance. Variant got 2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
BCL7A	NM_001024808.3	c.39_40delGG	p.Ala14fs	frameshift_variant	1/6	ENST00000261822.5	NP_001019979.1
BCL7A	NM_020993.5	c.39_40delGG	p.Ala14fs	frameshift_variant	1/6		NP_066273.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
BCL7A	ENST00000261822.5	c.39_40delGG	p.Ala14fs	frameshift_variant	1/6	1	NM_001024808.3	ENSP00000261822.5
BCL7A	ENST00000538010.5	c.39_40delGG	p.Ala14fs	frameshift_variant	1/6	1		ENSP00000445868.1
BCL7A	ENST00000432926.2	n.153_154delGG		non_coding_transcript_exon_variant	1/4	2

Frequencies

GnomAD3 genomes Cov.: 29

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome Cov.: 29

ClinVar

Significance: -

Submissions summary: Other:1

Revision: -

Submissions by phenotype

Neoplasm Other:1

-, criteria provided, single submitter

clinical testing

Center for Genomic Medicine, Rigshospitalet, Copenhagen University Hospital

Jul 31, 2024

- -

Computational scores

Source: dbNSFP v4.3

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

No publications associated with this variant yet.

Other links and lift over

hg19: chr12-122460034;