chr2-60553515-G-GGAGA
Variant summary
Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BA1
The NM_022893.4(BCL11A):c.-249_-246dupTCTC variant causes a 5 prime UTR 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 0.98 ( 39856 hom., cov: 0)
Exomes 𝑓: 0.94 ( 14768 hom. )
Consequence
BCL11A
NM_022893.4 5_prime_UTR
NM_022893.4 5_prime_UTR
Scores
Not classified
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 1.88
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 was made for transcript
Our verdict: Benign. The variant received -8 ACMG points.
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.978 is higher than 0.05.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.982 AC: 81100AN: 82600Hom.: 39840 Cov.: 0 show subpopulations
GnomAD3 genomes
AF:
AC:
81100
AN:
82600
Hom.:
Cov.:
0
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
GnomAD4 exome AF: 0.936 AC: 31084AN: 33218Hom.: 14768 Cov.: 0 AF XY: 0.938 AC XY: 17061AN XY: 18196 show subpopulations
GnomAD4 exome
AF:
AC:
31084
AN:
33218
Hom.:
Cov.:
0
AF XY:
AC XY:
17061
AN XY:
18196
show subpopulations
African (AFR)
AF:
AC:
116
AN:
132
American (AMR)
AF:
AC:
341
AN:
358
Ashkenazi Jewish (ASJ)
AF:
AC:
482
AN:
510
East Asian (EAS)
AF:
AC:
371
AN:
388
South Asian (SAS)
AF:
AC:
5980
AN:
6226
European-Finnish (FIN)
AF:
AC:
1768
AN:
2086
Middle Eastern (MID)
AF:
AC:
96
AN:
98
European-Non Finnish (NFE)
AF:
AC:
20246
AN:
21630
Other (OTH)
AF:
AC:
1684
AN:
1790
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.705
Heterozygous variant carriers
0
114
229
343
458
572
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
GnomAD4 genome AF: 0.982 AC: 81132AN: 82632Hom.: 39856 Cov.: 0 AF XY: 0.982 AC XY: 35570AN XY: 36230 show subpopulations
GnomAD4 genome
AF:
AC:
81132
AN:
82632
Hom.:
Cov.:
0
AF XY:
AC XY:
35570
AN XY:
36230
show subpopulations
African (AFR)
AF:
AC:
18432
AN:
18614
American (AMR)
AF:
AC:
5663
AN:
5740
Ashkenazi Jewish (ASJ)
AF:
AC:
2673
AN:
2710
East Asian (EAS)
AF:
AC:
2468
AN:
2480
South Asian (SAS)
AF:
AC:
1724
AN:
1740
European-Finnish (FIN)
AF:
AC:
1098
AN:
1204
Middle Eastern (MID)
AF:
AC:
113
AN:
114
European-Non Finnish (NFE)
AF:
AC:
47312
AN:
48364
Other (OTH)
AF:
AC:
1018
AN:
1026
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.596
Heterozygous variant carriers
0
49
99
148
198
247
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Alfa
AF:
Hom.:
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at