rs9604779

Variant names:

• chr22-17636379-T-C
• rs9604779
• ENST00000399782.5:c.-649-1723T>C

Variant summary

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

The ENST00000399782.5(BCL2L13):​c.-649-1723T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0786 in 150,892 control chromosomes in the GnomAD database, including 538 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 0.079 (538 hom., cov: 31)
• Consequence: BCL2L13 ENST00000399782.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0550

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=-0.63).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0908 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
BCL2L13	XM_011546119.2	c.-592-1723T>C		intron_variant	Intron 1 of 6		XP_011544421.1
BCL2L13	XM_011546120.2	c.-592-1723T>C		intron_variant	Intron 1 of 6		XP_011544422.1
BCL2L13	XM_047441286.1	c.-592-1723T>C		intron_variant	Intron 1 of 6		XP_047297242.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
BCL2L13	ENST00000399782.5	c.-649-1723T>C		intron_variant	Intron 1 of 6	1		ENSP00000382682.1
BCL2L13	ENST00000399781.5	n.53-1723T>C		intron_variant	Intron 1 of 4	3

Frequencies

GnomAD3 genomes AF: 0.0786 AC: 11852 AN: 150842 Hom.: 536 Cov.: 31

Gnomad AFR AF: 0.0933

Gnomad AMI AF: 0.0637

Gnomad AMR AF: 0.0477

Gnomad ASJ AF: 0.0516

Gnomad EAS AF: 0.00116

Gnomad SAS AF: 0.0499

Gnomad FIN AF: 0.0742

Gnomad MID AF: 0.0691

Gnomad NFE AF: 0.0869

Gnomad OTH AF: 0.0713

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

GnomAD4 genome AF: 0.0786 AC: 11856 AN: 150892 Hom.: 538 Cov.: 31 AF XY: 0.0755 AC XY: 5559 AN XY: 73594

Gnomad4 AFR AF: 0.0932

Gnomad4 AMR AF: 0.0475

Gnomad4 ASJ AF: 0.0516

Gnomad4 EAS AF: 0.00117

Gnomad4 SAS AF: 0.0497

Gnomad4 FIN AF: 0.0742

Gnomad4 NFE AF: 0.0870

Gnomad4 OTH AF: 0.0708

Alfa AF: 0.0894 Hom.: 80

Bravo AF: 0.0764

Asia WGS AF: 0.0290 AC: 102 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.63
CADD	Benign	3.1
DANN	Benign	0.67

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9604779; hg19: chr22-18119145;