rs8919

chr22-17730291-G-Achr22-17730291-G-Cchr22-17730291-G-T

Variant summary

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

The NM_015367.4(BCL2L13):c.*2757G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.449 in 151,924 control chromosomes in the GnomAD database, including 16,243 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 0.45 (16243 hom., cov: 31)
  • Exomes 𝑓: 0.15 (0 hom.)
• Consequence: BCL2L13 NM_015367.4 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.09

Genes affected

BCL2L13 (HGNC:17164): (BCL2 like 13) This gene encodes a mitochondrially-localized protein with conserved B-cell lymphoma 2 homology motifs. Overexpression of the encoded protein results in apoptosis. Alternatively spliced transcript variants have been observed for this gene. [provided by RefSeq, Jul 2012]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.787 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
BCL2L13	NM_015367.4	c.*2757G>A		3_prime_UTR_variant	7/7	ENST00000317582.10

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
BCL2L13	ENST00000317582.10	c.*2757G>A		3_prime_UTR_variant	7/7	1	NM_015367.4	A2

Frequencies

GnomAD3 genomes AF: 0.449 AC: 68173 AN: 151786 Hom.: 16243 Cov.: 31

Gnomad AFR AF: 0.346

Gnomad AMI AF: 0.586

Gnomad AMR AF: 0.562

Gnomad ASJ AF: 0.447

Gnomad EAS AF: 0.809

Gnomad SAS AF: 0.580

Gnomad FIN AF: 0.462

Gnomad MID AF: 0.421

Gnomad NFE AF: 0.446

Gnomad OTH AF: 0.454

GnomAD4 exome AF: 0.150 AC: 3 AN: 20 Hom.: 0 Cov.: 0 AF XY: 0.188 AC XY: 3 AN XY: 16

Gnomad4 AFR exome AF: 0.500

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.143

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome AF: 0.449 AC: 68209 AN: 151904 Hom.: 16243 Cov.: 31 AF XY: 0.457 AC XY: 33935 AN XY: 74230

Gnomad4 AFR AF: 0.346

Gnomad4 AMR AF: 0.562

Gnomad4 ASJ AF: 0.447

Gnomad4 EAS AF: 0.807

Gnomad4 SAS AF: 0.580

Gnomad4 FIN AF: 0.462

Gnomad4 NFE AF: 0.446

Gnomad4 OTH AF: 0.457

Alfa AF: 0.449 Hom.: 8546

Bravo AF: 0.456

Asia WGS AF: 0.659 AC: 2290 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
Cadd	Benign	0.30
Dann	Benign	0.76

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs8919; hg19: chr22-18213057;