rs74932682

Positions:

• chr22-17728062-T-A
• chr22-17728062-T-C

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_Strong BS2

The NM_015367.4(BCL2L13):​c.*528T>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 0.00669 in 160,564 control chromosomes in the GnomAD database, including 8 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 0.0067 (7 hom., cov: 32)
  • Exomes 𝑓: 0.0062 (1 hom.)
• Consequence: BCL2L13 NM_015367.4 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0150

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 -8 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BS2: High Homozygotes in GnomAd4 at 7 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
BCL2L13	NM_015367.4	c.*528T>A		3_prime_UTR_variant	7/7	ENST00000317582.10	NP_056182.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
BCL2L13	ENST00000317582.10	c.*528T>A		3_prime_UTR_variant	7/7	1	NM_015367.4	ENSP00000318883	A2

Frequencies

GnomAD3 genomes AF: 0.00672 AC: 1023 AN: 152162 Hom.: 7 Cov.: 32

Gnomad AFR AF: 0.00130

Gnomad AMI AF: 0.00439

Gnomad AMR AF: 0.00236

Gnomad ASJ AF: 0.00403

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.0306

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00852

Gnomad OTH AF: 0.00478

GnomAD4 exome AF: 0.00616 AC: 51 AN: 8284 Hom.: 1 Cov.: 0 AF XY: 0.00714 AC XY: 31 AN XY: 4344

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.00483

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.0179

Gnomad4 NFE exome AF: 0.00889

Gnomad4 OTH exome AF: 0.0103

GnomAD4 genome AF: 0.00672 AC: 1023 AN: 152280 Hom.: 7 Cov.: 32 AF XY: 0.00749 AC XY: 558 AN XY: 74450

Gnomad4 AFR AF: 0.00130

Gnomad4 AMR AF: 0.00235

Gnomad4 ASJ AF: 0.00403

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00

Gnomad4 FIN AF: 0.0306

Gnomad4 NFE AF: 0.00853

Gnomad4 OTH AF: 0.00473

Alfa AF: 0.00357 Hom.: 0

Bravo AF: 0.00441

Asia WGS AF: 0.000289 AC: 1 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	1.2
DANN	Benign	0.61

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: rs74932682; hg19: chr22-18210828;