rs11886868
Positions:
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_022893.4(BCL11A):c.386-24278G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.634 in 152,036 control chromosomes in the GnomAD database, including 32,265 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Genomes: 𝑓 0.63 ( 32265 hom., cov: 31)
Consequence
BCL11A
NM_022893.4 intron
NM_022893.4 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.837
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]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -20 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.87).
BP6
?
Variant 2-60493111-C-T is Benign according to our data. Variant chr2-60493111-C-T is described in ClinVar as [Benign]. Clinvar id is 127265.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.705 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
BCL11A | NM_022893.4 | c.386-24278G>A | intron_variant | ENST00000642384.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
BCL11A | ENST00000642384.2 | c.386-24278G>A | intron_variant | NM_022893.4 |
Frequencies
GnomAD3 genomes ? AF: 0.634 AC: 96347AN: 151918Hom.: 32238 Cov.: 31
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome ? AF: 0.634 AC: 96415AN: 152036Hom.: 32265 Cov.: 31 AF XY: 0.619 AC XY: 45978AN XY: 74310
GnomAD4 genome
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984
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3478
ClinVar
Significance: Benign
Submissions summary: Pathogenic:1Benign:3
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
Dias-Logan syndrome Benign:2
Benign, criteria provided, single submitter | clinical testing | Mendelics | May 28, 2019 | - - |
Benign, no assertion criteria provided | curation | Reproductive Health Research and Development, BGI Genomics | Jan 06, 2020 | NG_011968.1(NM_018014.3):c.386-24278G>A in the BCL11A gene has an allele frequency of 0.713 in African subpopulation in the gnomAD database. This evidence suggests the variant to be classified as benign. ACMG/AMP criteria applied: BA1. - |
Fetal hemoglobin quantitative trait locus 5 Pathogenic:1
Likely pathogenic, no assertion criteria provided | literature only | Genomic Research Center, Shahid Beheshti University of Medical Sciences | - | - - |
not specified Benign:1
Benign, criteria provided, single submitter | research | H3Africa Consortium | Oct 28, 2020 | While the frequency of the alternate allele in gnoMAD v2.0.2 is 0.8, its frequency in African populations is >5%. This suggests that previous classifications of this variant as pathogenic are in error. - |
Computational scores
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Name
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at