rs9604779

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 4 publications found

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

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000399782.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	BCL2L13	ENST00000399782.5	TSL:1	c.-649-1723T>C		intron	N/A	ENSP00000382682.1	Q9BXK5-2
	BCL2L13	ENST00000870790.1		c.-51+7473T>C		intron	N/A	ENSP00000540849.1
	BCL2L13	ENST00000870791.1		c.-649-1723T>C		intron	N/A	ENSP00000540850.1

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

African (AFR) AF: 0.0932 AC: 3833 AN: 41112

American (AMR) AF: 0.0475 AC: 718 AN: 15112

Ashkenazi Jewish (ASJ) AF: 0.0516 AC: 178 AN: 3452

East Asian (EAS) AF: 0.00117 AC: 6 AN: 5138

South Asian (SAS) AF: 0.0497 AC: 236 AN: 4748

European-Finnish (FIN) AF: 0.0742 AC: 756 AN: 10188

Middle Eastern (MID) AF: 0.0780 AC: 22 AN: 282

European-Non Finnish (NFE) AF: 0.0870 AC: 5901 AN: 67860

Other (OTH) AF: 0.0708 AC: 148 AN: 2090

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.63
CADD	Benign	3.1
DANN	Benign	0.67
PhyloP100		0.055
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs9604779;

hg19: chr22-18119145;