12-122022128-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

Scores

Not classified

Clinical Significance

- - O:1

Conservation

PhyloP100: 5.73
Variant links:
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]

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ACMG classification

Classification made for transcript

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
BCL7ANM_001024808.3 linkuse as main transcriptc.39_40delGG p.Ala14fs frameshift_variant 1/6 ENST00000261822.5 NP_001019979.1 Q4VC05-1
BCL7ANM_020993.5 linkuse as main transcriptc.39_40delGG p.Ala14fs frameshift_variant 1/6 NP_066273.1 Q4VC05-2

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
BCL7AENST00000261822.5 linkuse as main transcriptc.39_40delGG p.Ala14fs frameshift_variant 1/61 NM_001024808.3 ENSP00000261822.5 Q4VC05-1
BCL7AENST00000538010.5 linkuse as main transcriptc.39_40delGG p.Ala14fs frameshift_variant 1/61 ENSP00000445868.1 Q4VC05-2
BCL7AENST00000432926.2 linkuse as main transcriptn.153_154delGG non_coding_transcript_exon_variant 1/42

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: -
LINK: link

Submissions by phenotype

Neoplasm Other:1
-, criteria provided, single submitterclinical testingCenter for Genomic Medicine, Rigshospitalet, Copenhagen University HospitalJul 31, 2024- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction

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; API