chr12-122043384-G-T

Variant names:

• chr12-122043384-G-T
• rs12827036
• NM_001024808.3:c.272-502G>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001024808.3(BCL7A):​c.272-502G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.34 (10019 hom., cov: 20)
• Consequence: BCL7A NM_001024808.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.783
• Publications: 7 publications found

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]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.477 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
BCL7A	NM_001024808.3	c.272-502G>T		intron_variant	Intron 3 of 5	ENST00000261822.5	NP_001019979.1
BCL7A	NM_020993.5	c.272-502G>T		intron_variant	Intron 3 of 5		NP_066273.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
BCL7A	ENST00000261822.5	c.272-502G>T		intron_variant	Intron 3 of 5	1	NM_001024808.3	ENSP00000261822.5
BCL7A	ENST00000538010.5	c.272-502G>T		intron_variant	Intron 3 of 5	1		ENSP00000445868.1
BCL7A	ENST00000432926.2	n.386-502G>T		intron_variant	Intron 3 of 3	2

Frequencies

GnomAD3 genomes AF: 0.340 AC: 47167 AN: 138712 Hom.: 10022 Cov.: 20

Gnomad AFR AF: 0.110

Gnomad AMI AF: 0.481

Gnomad AMR AF: 0.291

Gnomad ASJ AF: 0.446

Gnomad EAS AF: 0.00285

Gnomad SAS AF: 0.203

Gnomad FIN AF: 0.470

Gnomad MID AF: 0.405

Gnomad NFE AF: 0.481

Gnomad OTH AF: 0.343

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

GnomAD4 genome AF: 0.340 AC: 47153 AN: 138816 Hom.: 10019 Cov.: 20 AF XY: 0.335 AC XY: 22428 AN XY: 66920

African (AFR) AF: 0.110 AC: 3925 AN: 35638

American (AMR) AF: 0.290 AC: 3935 AN: 13550

Ashkenazi Jewish (ASJ) AF: 0.446 AC: 1505 AN: 3374

East Asian (EAS) AF: 0.00285 AC: 13 AN: 4554

South Asian (SAS) AF: 0.202 AC: 824 AN: 4072

European-Finnish (FIN) AF: 0.470 AC: 4406 AN: 9376

Middle Eastern (MID) AF: 0.404 AC: 114 AN: 282

European-Non Finnish (NFE) AF: 0.481 AC: 31386 AN: 65244

Other (OTH) AF: 0.338 AC: 631 AN: 1866

Alfa AF: 0.428 Hom.: 7905

Bravo AF: 0.306

Asia WGS AF: 0.0870 AC: 302 AN: 3446

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	4.5
DANN	Benign	0.64
PhyloP100		0.78
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs12827036; hg19: chr12-122481290;