rs34211119

Variant names:

• chr2-60493183-GT-G
• rs34211119
• NM_022893.4:c.386-24351delA

Variant summary

Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BA1

The NM_022893.4(BCL11A):​c.386-24351delA variant causes a intron change involving the alteration of a non-conserved nucleotide. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.63 (32010 hom., cov: 0)
• Consequence: BCL11A NM_022893.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.452
• Publications: 3 publications found

Genes affected

BCL11A (HGNC:13221): (BCL11 transcription factor A) This gene encodes a C2H2 type zinc-finger protein by its similarity to the mouse Bcl11a/Evi9 protein. The corresponding mouse gene is a common site of retroviral integration in myeloid leukemia, and may function as a leukemia disease gene, in part, through its interaction with BCL6. During hematopoietic cell differentiation, this gene is down-regulated. It is possibly involved in lymphoma pathogenesis since translocations associated with B-cell malignancies also deregulates its expression. Multiple transcript variants encoding several different isoforms have been found for this gene. [provided by RefSeq, Jul 2008]

BCL11A Gene-Disease associations (from GenCC):

• Dias-Logan syndrome

  Inheritance: AD Classification: DEFINITIVE, STRONG, MODERATE Submitted by: Labcorp Genetics (formerly Invitae), Illumina, ClinGen, PanelApp Australia, Ambry Genetics, G2P

ACMG classification

Our verdict: Benign. The variant received -8 ACMG points.

• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.697 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_022893.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	BCL11A	NM_022893.4	MANE Select	c.386-24351delA		intron	N/A	NP_075044.2
	BCL11A	NM_001405708.1		c.386-24351delA		intron	N/A	NP_001392637.1	D9YZW0
	BCL11A	NM_001405709.1		c.386-24351delA		intron	N/A	NP_001392638.1	D9YZW0

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	BCL11A	ENST00000642384.2	MANE Select	c.386-24351delA		intron	N/A	ENSP00000496168.1	Q9H165-1
	BCL11A	ENST00000335712.11	TSL:1	c.386-30760delA		intron	N/A	ENSP00000338774.7	Q9H165-6
	BCL11A	ENST00000358510.6	TSL:1	c.386-30760delA		intron	N/A	ENSP00000351307.5	A0A2U3TZJ5

Frequencies

GnomAD3 genomes AF: 0.632 AC: 95985 AN: 151890 Hom.: 31988 Cov.: 0

Gnomad AFR AF: 0.703

Gnomad AMI AF: 0.570

Gnomad AMR AF: 0.487

Gnomad ASJ AF: 0.570

Gnomad EAS AF: 0.0301

Gnomad SAS AF: 0.417

Gnomad FIN AF: 0.607

Gnomad MID AF: 0.611

Gnomad NFE AF: 0.690

Gnomad OTH AF: 0.625

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

GnomAD4 genome AF: 0.632 AC: 96048 AN: 152008 Hom.: 32010 Cov.: 0 AF XY: 0.616 AC XY: 45810 AN XY: 74318

African (AFR) AF: 0.703 AC: 29160 AN: 41456

American (AMR) AF: 0.486 AC: 7428 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.570 AC: 1978 AN: 3468

East Asian (EAS) AF: 0.0300 AC: 155 AN: 5172

South Asian (SAS) AF: 0.415 AC: 2003 AN: 4822

European-Finnish (FIN) AF: 0.607 AC: 6418 AN: 10570

Middle Eastern (MID) AF: 0.599 AC: 176 AN: 294

European-Non Finnish (NFE) AF: 0.690 AC: 46908 AN: 67940

Other (OTH) AF: 0.619 AC: 1304 AN: 2108

Alfa AF: 0.667 Hom.: 3730

Bravo AF: 0.622

Asia WGS AF: 0.283 AC: 987 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		-0.45
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: rs34211119; hg19: chr2-60720318;