rs2058703

chr2-60452091-G-Achr2-60452091-G-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000356842.9(BCL11A):c.*484C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.632 in 227,174 control chromosomes in the GnomAD database, including 46,879 homozygotes. 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 0.63 (30827 hom., cov: 33)
  • Exomes 𝑓: 0.64 (16052 hom.)
• Consequence: BCL11A ENST00000356842.9 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.664

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.955 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
BCL11A	NM_001363864.1	c.*474C>T		3_prime_UTR_variant	4/4
BCL11A	NM_018014.4	c.*484C>T		3_prime_UTR_variant	5/5
BCL11A	NM_138559.2	c.*474C>T		3_prime_UTR_variant	5/5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
BCL11A	ENST00000356842.9	c.*484C>T		3_prime_UTR_variant	5/5	1
BCL11A	ENST00000359629.10	c.*474C>T		3_prime_UTR_variant	5/5	1
BCL11A	ENST00000489516.7	c.*474C>T		3_prime_UTR_variant	5/5	5

Frequencies

GnomAD3 genomes AF: 0.629 AC: 95680 AN: 152008 Hom.: 30797 Cov.: 33

Gnomad AFR AF: 0.679

Gnomad AMI AF: 0.641

Gnomad AMR AF: 0.710

Gnomad ASJ AF: 0.490

Gnomad EAS AF: 0.977

Gnomad SAS AF: 0.568

Gnomad FIN AF: 0.588

Gnomad MID AF: 0.478

Gnomad NFE AF: 0.573

Gnomad OTH AF: 0.612

GnomAD4 exome AF: 0.636 AC: 47723 AN: 75048 Hom.: 16052 Cov.: 0 AF XY: 0.631 AC XY: 21927 AN XY: 34730

Gnomad4 AFR exome AF: 0.672

Gnomad4 AMR exome AF: 0.749

Gnomad4 ASJ exome AF: 0.508

Gnomad4 EAS exome AF: 0.979

Gnomad4 SAS exome AF: 0.552

Gnomad4 FIN exome AF: 0.558

Gnomad4 NFE exome AF: 0.568

Gnomad4 OTH exome AF: 0.611

GnomAD4 genome AF: 0.629 AC: 95762 AN: 152126 Hom.: 30827 Cov.: 33 AF XY: 0.630 AC XY: 46851 AN XY: 74358

Gnomad4 AFR AF: 0.679

Gnomad4 AMR AF: 0.711

Gnomad4 ASJ AF: 0.490

Gnomad4 EAS AF: 0.978

Gnomad4 SAS AF: 0.568

Gnomad4 FIN AF: 0.588

Gnomad4 NFE AF: 0.573

Gnomad4 OTH AF: 0.610

Alfa AF: 0.588 Hom.: 34221

Bravo AF: 0.647

Asia WGS AF: 0.741 AC: 2576 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
Cadd	Benign	2.7
Dann	Benign	0.67

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2058703; hg19: chr2-60679226;