NM_138621.5:c.498+4957C>A
Variant names:
Variant summary
Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_138621.5(BCL2L11):c.498+4957C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.585 in 152,086 control chromosomes in the GnomAD database, including 27,991 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 0.58 ( 27991 hom., cov: 33)
Consequence
BCL2L11
NM_138621.5 intron
NM_138621.5 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -2.49
Publications
11 publications found
Genes affected
BCL2L11 (HGNC:994): (BCL2 like 11) The protein encoded by this gene belongs to the BCL-2 protein family. BCL-2 family members form hetero- or homodimers and act as anti- or pro-apoptotic regulators that are involved in a wide variety of cellular activities. The protein encoded by this gene contains a Bcl-2 homology domain 3 (BH3). It has been shown to interact with other members of the BCL-2 protein family and to act as an apoptotic activator. The expression of this gene can be induced by nerve growth factor (NGF), as well as by the forkhead transcription factor FKHR-L1, which suggests a role of this gene in neuronal and lymphocyte apoptosis. Transgenic studies of the mouse counterpart suggested that this gene functions as an essential initiator of apoptosis in thymocyte-negative selection. Several alternatively spliced transcript variants of this gene have been identified. [provided by RefSeq, Jun 2013]
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ACMG classification
Classification was made for transcript
Our verdict: Benign. The variant received -12 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.88).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.815 is higher than 0.05.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes 0.585 AC: 88840AN: 151968Hom.: 27945 Cov.: 33 show subpopulations
GnomAD3 genomes
AF:
AC:
88840
AN:
151968
Hom.:
Cov.:
33
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:
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome 0.585 AC: 88938AN: 152086Hom.: 27991 Cov.: 33 AF XY: 0.575 AC XY: 42719AN XY: 74344 show subpopulations
GnomAD4 genome
AF:
AC:
88938
AN:
152086
Hom.:
Cov.:
33
AF XY:
AC XY:
42719
AN XY:
74344
show subpopulations
African (AFR)
AF:
AC:
34166
AN:
41526
American (AMR)
AF:
AC:
6041
AN:
15272
Ashkenazi Jewish (ASJ)
AF:
AC:
1406
AN:
3466
East Asian (EAS)
AF:
AC:
2829
AN:
5168
South Asian (SAS)
AF:
AC:
1460
AN:
4824
European-Finnish (FIN)
AF:
AC:
5418
AN:
10544
Middle Eastern (MID)
AF:
AC:
94
AN:
294
European-Non Finnish (NFE)
AF:
AC:
35956
AN:
67968
Other (OTH)
AF:
AC:
1101
AN:
2112
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.503
Heterozygous variant carriers
0
1776
3552
5327
7103
8879
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Age Distribution
Genome Het
Genome Hom
Variant carriers
0
718
1436
2154
2872
3590
<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:
Hom.:
Bravo
AF:
Asia WGS
AF:
AC:
1433
AN:
3478
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
DANN
Benign
PhyloP100
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
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