20-31673759-G-C

Variant names:

• chr20-31673759-G-C
• rs6060621
• NM_138578.3:c.565-7673C>G

Variant summary

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

The NM_138578.3(BCL2L1):​c.565-7673C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.369 in 152,056 control chromosomes in the GnomAD database, including 12,432 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 0.37 (12432 hom., cov: 31)
• Consequence: BCL2L1 NM_138578.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.184
• Publications: 3 publications found

Genes affected

BCL2L1 (HGNC:992): (BCL2 like 1) The protein encoded by this gene belongs to the BCL-2 protein family. BCL-2 family members form hetero- or homodimers and act as anti- or pro-apoptotic regulators that are involved in a wide variety of cellular activities. The proteins encoded by this gene are located at the outer mitochondrial membrane, and have been shown to regulate outer mitochondrial membrane channel (VDAC) opening. VDAC regulates mitochondrial membrane potential, and thus controls the production of reactive oxygen species and release of cytochrome C by mitochondria, both of which are the potent inducers of cell apoptosis. Alternative splicing results in multiple transcript variants encoding two different isoforms. The longer isoform acts as an apoptotic inhibitor and the shorter isoform acts as an apoptotic activator. [provided by RefSeq, Dec 2015]

LOC124904883 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.603 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
BCL2L1	NM_138578.3	c.565-7673C>G		intron_variant	Intron 2 of 2	ENST00000307677.5	NP_612815.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
BCL2L1	ENST00000307677.5	c.565-7673C>G		intron_variant	Intron 2 of 2	1	NM_138578.3	ENSP00000302564.4

Frequencies

GnomAD3 genomes AF: 0.369 AC: 56023 AN: 151938 Hom.: 12411 Cov.: 31

Gnomad AFR AF: 0.610

Gnomad AMI AF: 0.188

Gnomad AMR AF: 0.267

Gnomad ASJ AF: 0.332

Gnomad EAS AF: 0.00173

Gnomad SAS AF: 0.0892

Gnomad FIN AF: 0.393

Gnomad MID AF: 0.237

Gnomad NFE AF: 0.295

Gnomad OTH AF: 0.348

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

GnomAD4 genome AF: 0.369 AC: 56090 AN: 152056 Hom.: 12432 Cov.: 31 AF XY: 0.364 AC XY: 27028 AN XY: 74340

African (AFR) AF: 0.610 AC: 25256 AN: 41426

American (AMR) AF: 0.266 AC: 4070 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.332 AC: 1153 AN: 3470

East Asian (EAS) AF: 0.00173 AC: 9 AN: 5192

South Asian (SAS) AF: 0.0895 AC: 432 AN: 4828

European-Finnish (FIN) AF: 0.393 AC: 4145 AN: 10556

Middle Eastern (MID) AF: 0.241 AC: 71 AN: 294

European-Non Finnish (NFE) AF: 0.295 AC: 20054 AN: 67972

Other (OTH) AF: 0.345 AC: 729 AN: 2112

Alfa AF: 0.343 Hom.: 1264

Bravo AF: 0.375

Asia WGS AF: 0.0810 AC: 285 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.7
DANN	Benign	0.56
PhyloP100		0.18
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: rs6060621; hg19: chr20-30261562;