18-63257380-A-T

Position:

• chr18-63257380-A-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_000633.3(BCL2):​c.585+60702T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.412 in 152,182 control chromosomes in the GnomAD database, including 13,815 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 0.41 (13815 hom., cov: 33)
• Consequence: BCL2 NM_000633.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.670

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

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.68).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.593 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
BCL2	NM_000633.3	c.585+60702T>A		intron_variant		ENST00000333681.5
BCL2	XM_047437733.1	c.585+60702T>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
BCL2	ENST00000333681.5	c.585+60702T>A		intron_variant		1	NM_000633.3	P1

Frequencies

GnomAD3 genomes AF: 0.412 AC: 62663 AN: 152062 Hom.: 13805 Cov.: 33

Gnomad AFR AF: 0.263

Gnomad AMI AF: 0.454

Gnomad AMR AF: 0.416

Gnomad ASJ AF: 0.504

Gnomad EAS AF: 0.589

Gnomad SAS AF: 0.611

Gnomad FIN AF: 0.365

Gnomad MID AF: 0.462

Gnomad NFE AF: 0.476

Gnomad OTH AF: 0.426

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

GnomAD4 genome AF: 0.412 AC: 62708 AN: 152182 Hom.: 13815 Cov.: 33 AF XY: 0.412 AC XY: 30655 AN XY: 74404

Gnomad4 AFR AF: 0.263

Gnomad4 AMR AF: 0.416

Gnomad4 ASJ AF: 0.504

Gnomad4 EAS AF: 0.588

Gnomad4 SAS AF: 0.611

Gnomad4 FIN AF: 0.365

Gnomad4 NFE AF: 0.476

Gnomad4 OTH AF: 0.428

Alfa AF: 0.433 Hom.: 1821

Bravo AF: 0.403

Asia WGS AF: 0.559 AC: 1941 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.68
CADD	Benign	11
DANN	Benign	0.84

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

Publications

LitVar

Other links and lift over

dbSNP: rs1944419; hg19: chr18-60924613;