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

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.88
Variant links:
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]

Genome browser will be placed here

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

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
BCL11ANM_022893.4 linkc.-249_-246dupTCTC 5_prime_UTR_variant Exon 1 of 4 ENST00000642384.2 NP_075044.2 Q9H165-1D9YZW0

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
BCL11AENST00000642384.2 linkc.-249_-246dupTCTC 5_prime_UTR_variant Exon 1 of 4 NM_022893.4 ENSP00000496168.1 Q9H165-1

Frequencies

GnomAD3 genomes
AF:
0.982
AC:
81100
AN:
82600
Hom.:
39840
Cov.:
0
show subpopulations
Gnomad AFR
AF:
0.990
Gnomad AMI
AF:
0.986
Gnomad AMR
AF:
0.987
Gnomad ASJ
AF:
0.986
Gnomad EAS
AF:
0.995
Gnomad SAS
AF:
0.990
Gnomad FIN
AF:
0.912
Gnomad MID
AF:
0.992
Gnomad NFE
AF:
0.978
Gnomad OTH
AF:
0.992
GnomAD4 exome
AF:
0.936
AC:
31084
AN:
33218
Hom.:
14768
Cov.:
0
AF XY:
0.938
AC XY:
17061
AN XY:
18196
show subpopulations
African (AFR)
AF:
0.879
AC:
116
AN:
132
American (AMR)
AF:
0.953
AC:
341
AN:
358
Ashkenazi Jewish (ASJ)
AF:
0.945
AC:
482
AN:
510
East Asian (EAS)
AF:
0.956
AC:
371
AN:
388
South Asian (SAS)
AF:
0.960
AC:
5980
AN:
6226
European-Finnish (FIN)
AF:
0.848
AC:
1768
AN:
2086
Middle Eastern (MID)
AF:
0.980
AC:
96
AN:
98
European-Non Finnish (NFE)
AF:
0.936
AC:
20246
AN:
21630
Other (OTH)
AF:
0.941
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

Age Distribution

Exome Het
Exome Hom
Variant carriers
0
32
64
96
128
160
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
GnomAD4 genome
AF:
0.982
AC:
81132
AN:
82632
Hom.:
39856
Cov.:
0
AF XY:
0.982
AC XY:
35570
AN XY:
36230
show subpopulations
African (AFR)
AF:
0.990
AC:
18432
AN:
18614
American (AMR)
AF:
0.987
AC:
5663
AN:
5740
Ashkenazi Jewish (ASJ)
AF:
0.986
AC:
2673
AN:
2710
East Asian (EAS)
AF:
0.995
AC:
2468
AN:
2480
South Asian (SAS)
AF:
0.991
AC:
1724
AN:
1740
European-Finnish (FIN)
AF:
0.912
AC:
1098
AN:
1204
Middle Eastern (MID)
AF:
0.991
AC:
113
AN:
114
European-Non Finnish (NFE)
AF:
0.978
AC:
47312
AN:
48364
Other (OTH)
AF:
0.992
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

Age Distribution

Genome Het
Genome Hom
Variant carriers
0
482
964
1446
1928
2410
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
Alfa
AF:
0.00
Hom.:
0

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
Mutation Taster
=300/0
polymorphism (auto)

Splicing

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs113296120; hg19: chr2-60780650; API