chr18-63268814-A-G
Variant names:
Variant summary
Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_000633.3(BCL2):c.585+49268T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.18 in 152,156 control chromosomes in the GnomAD database, including 2,982 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 0.18 ( 2982 hom., cov: 32)
Consequence
BCL2
NM_000633.3 intron
NM_000633.3 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.771
Publications
13 publications found
Genes affected
BCL2 (HGNC:990): (BCL2 apoptosis regulator) This gene encodes an integral outer mitochondrial membrane protein that blocks the apoptotic death of some cells such as lymphocytes. Constitutive expression of BCL2, such as in the case of translocation of BCL2 to Ig heavy chain locus, is thought to be the cause of follicular lymphoma. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Feb 2016]
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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=-0.75).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.376 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
BCL2 | NM_000633.3 | c.585+49268T>C | intron_variant | Intron 2 of 2 | ENST00000333681.5 | NP_000624.2 | ||
BCL2 | XM_047437733.1 | c.585+49268T>C | intron_variant | Intron 1 of 1 | XP_047293689.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.180 AC: 27393AN: 152038Hom.: 2981 Cov.: 32 show subpopulations
GnomAD3 genomes
AF:
AC:
27393
AN:
152038
Hom.:
Cov.:
32
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 AF: 0.180 AC: 27392AN: 152156Hom.: 2982 Cov.: 32 AF XY: 0.182 AC XY: 13525AN XY: 74374 show subpopulations
GnomAD4 genome
AF:
AC:
27392
AN:
152156
Hom.:
Cov.:
32
AF XY:
AC XY:
13525
AN XY:
74374
show subpopulations
African (AFR)
AF:
AC:
3221
AN:
41536
American (AMR)
AF:
AC:
2257
AN:
15288
Ashkenazi Jewish (ASJ)
AF:
AC:
644
AN:
3468
East Asian (EAS)
AF:
AC:
2017
AN:
5172
South Asian (SAS)
AF:
AC:
1534
AN:
4814
European-Finnish (FIN)
AF:
AC:
2441
AN:
10554
Middle Eastern (MID)
AF:
AC:
42
AN:
294
European-Non Finnish (NFE)
AF:
AC:
14762
AN:
68008
Other (OTH)
AF:
AC:
348
AN:
2112
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.501
Heterozygous variant carriers
0
1121
2242
3364
4485
5606
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Age Distribution
Genome Het
Genome Hom
Variant carriers
0
320
640
960
1280
1600
<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:
1075
AN:
3476
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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