NM_000633.3:c.586-18923T>G

Variant names:

• chr18-63147682-A-C
• rs1542578
• NM_000633.3:c.586-18923T>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_000633.3(BCL2):​c.586-18923T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.599 in 151,984 control chromosomes in the GnomAD database, including 28,085 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 0.60 (28085 hom., cov: 32)
• Consequence: BCL2 NM_000633.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.688
• Publications: 8 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]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.77).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.746 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
BCL2	NM_000633.3	c.586-18923T>G		intron_variant	Intron 2 of 2	ENST00000333681.5	NP_000624.2
BCL2	XM_047437733.1	c.586-18923T>G		intron_variant	Intron 1 of 1		XP_047293689.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
BCL2	ENST00000333681.5	c.586-18923T>G		intron_variant	Intron 2 of 2	1	NM_000633.3	ENSP00000329623.3

Frequencies

GnomAD3 genomes AF: 0.599 AC: 90908 AN: 151866 Hom.: 28039 Cov.: 32

Gnomad AFR AF: 0.753

Gnomad AMI AF: 0.480

Gnomad AMR AF: 0.531

Gnomad ASJ AF: 0.586

Gnomad EAS AF: 0.627

Gnomad SAS AF: 0.621

Gnomad FIN AF: 0.488

Gnomad MID AF: 0.576

Gnomad NFE AF: 0.536

Gnomad OTH AF: 0.593

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.599 AC: 91006 AN: 151984 Hom.: 28085 Cov.: 32 AF XY: 0.596 AC XY: 44284 AN XY: 74314

African (AFR) AF: 0.753 AC: 31216 AN: 41446

American (AMR) AF: 0.531 AC: 8119 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.586 AC: 2029 AN: 3464

East Asian (EAS) AF: 0.626 AC: 3235 AN: 5164

South Asian (SAS) AF: 0.620 AC: 2979 AN: 4806

European-Finnish (FIN) AF: 0.488 AC: 5153 AN: 10562

Middle Eastern (MID) AF: 0.575 AC: 168 AN: 292

European-Non Finnish (NFE) AF: 0.536 AC: 36418 AN: 67950

Other (OTH) AF: 0.593 AC: 1251 AN: 2108

Alfa AF: 0.460 Hom.: 1997

Bravo AF: 0.607

Asia WGS AF: 0.582 AC: 2021 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.77
CADD	Benign	2.9
DANN	Benign	0.80
PhyloP100		-0.69
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs1542578; hg19: chr18-60814915;