rs1801018
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Variant summary
Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_StrongBP6_ModerateBP7BA1
The NM_000633.3(BCL2):āc.21A>Gā(p.Thr7=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.398 in 1,612,024 control chromosomes in the GnomAD database, including 135,183 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (ā ).
Frequency
Genomes: š 0.32 ( 9647 hom., cov: 32)
Exomes š: 0.41 ( 125536 hom. )
Consequence
BCL2
NM_000633.3 synonymous
NM_000633.3 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.699
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 made for transcript
Verdict is Benign. Variant got -15 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.7).
BP6
?
Variant 18-63318646-T-C is Benign according to our data. Variant chr18-63318646-T-C is described in ClinVar as [Benign]. Clinvar id is 3060318.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
Synonymous conserved (PhyloP=0.699 with no splicing effect.
BA1
?
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.43 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
BCL2 | NM_000633.3 | c.21A>G | p.Thr7= | synonymous_variant | 2/3 | ENST00000333681.5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
BCL2 | ENST00000333681.5 | c.21A>G | p.Thr7= | synonymous_variant | 2/3 | 1 | NM_000633.3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.318 AC: 48421AN: 152080Hom.: 9644 Cov.: 32
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GnomAD3 exomes AF: 0.372 AC: 91756AN: 246918Hom.: 18853 AF XY: 0.378 AC XY: 50836AN XY: 134404
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GnomAD4 exome AF: 0.406 AC: 593323AN: 1459826Hom.: 125536 Cov.: 65 AF XY: 0.407 AC XY: 295512AN XY: 726246
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GnomAD4 genome ? AF: 0.318 AC: 48426AN: 152198Hom.: 9647 Cov.: 32 AF XY: 0.320 AC XY: 23836AN XY: 74428
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
BCL2-related disorder Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Oct 16, 2019 | This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Computational scores
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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