rs9959874

chr18-63227313-G-Achr18-63227313-G-C

Variant summary

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

The NM_000633.3(BCL2):c.585+90769C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0845 in 152,258 control chromosomes in the GnomAD database, including 572 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 0.085 (572 hom., cov: 32)
• Consequence: BCL2 NM_000633.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.335

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=-0.69).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.152 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
BCL2	NM_000633.3	c.585+90769C>T		intron_variant		ENST00000333681.5
BCL2	XM_047437733.1	c.585+90769C>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
BCL2	ENST00000333681.5	c.585+90769C>T		intron_variant		1	NM_000633.3	P1

Frequencies

GnomAD3 genomes AF: 0.0844 AC: 12848 AN: 152140 Hom.: 568 Cov.: 32

Gnomad AFR AF: 0.0957

Gnomad AMI AF: 0.0537

Gnomad AMR AF: 0.0869

Gnomad ASJ AF: 0.0764

Gnomad EAS AF: 0.114

Gnomad SAS AF: 0.160

Gnomad FIN AF: 0.0931

Gnomad MID AF: 0.0981

Gnomad NFE AF: 0.0689

Gnomad OTH AF: 0.0813

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

GnomAD4 genome AF: 0.0845 AC: 12871 AN: 152258 Hom.: 572 Cov.: 32 AF XY: 0.0869 AC XY: 6471 AN XY: 74438

Gnomad4 AFR AF: 0.0957

Gnomad4 AMR AF: 0.0872

Gnomad4 ASJ AF: 0.0764

Gnomad4 EAS AF: 0.113

Gnomad4 SAS AF: 0.162

Gnomad4 FIN AF: 0.0931

Gnomad4 NFE AF: 0.0689

Gnomad4 OTH AF: 0.0856

Alfa AF: 0.0752 Hom.: 74

Bravo AF: 0.0837

Asia WGS AF: 0.127 AC: 440 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.69
Cadd	Benign	6.6
Dann	Benign	0.86

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: rs9959874; hg19: chr18-60894546;