22-17730291-G-A

Variant names:

• chr22-17730291-G-A
• rs8919
• ENST00000399777.2:n.*3713G>A

Variant summary

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

The ENST00000399777.2(BCL2L13):​n.*3713G>A variant causes a non coding transcript exon 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 ENST00000399777.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.09
• Publications: 15 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=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.787 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000399777.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	BCL2L13	NM_015367.4	MANE Select	c.*2757G>A		3_prime_UTR	Exon 7 of 7	NP_056182.2
	BCL2L13	NR_073068.1		n.4166G>A		non_coding_transcript_exon	Exon 5 of 5
	BCL2L13	NR_073069.1		n.4149G>A		non_coding_transcript_exon	Exon 5 of 5

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	BCL2L13	ENST00000399777.2	TSL:1	n.*3713G>A		non_coding_transcript_exon	Exon 6 of 6	ENSP00000382677.2
	BCL2L13	ENST00000317582.10	TSL:1 MANE Select	c.*2757G>A		3_prime_UTR	Exon 7 of 7	ENSP00000318883.5
	BCL2L13	ENST00000355028.4	TSL:1	c.*3485G>A		3_prime_UTR	Exon 5 of 5	ENSP00000347133.3

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

African (AFR) AF: 0.500 AC: 1 AN: 2

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 2

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.143 AC: 2 AN: 14

Other (OTH) AF: 0.00 AC: 0 AN: 2

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

African (AFR) AF: 0.346 AC: 14322 AN: 41410

American (AMR) AF: 0.562 AC: 8588 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.447 AC: 1551 AN: 3468

East Asian (EAS) AF: 0.807 AC: 4165 AN: 5158

South Asian (SAS) AF: 0.580 AC: 2793 AN: 4816

European-Finnish (FIN) AF: 0.462 AC: 4867 AN: 10540

Middle Eastern (MID) AF: 0.408 AC: 120 AN: 294

European-Non Finnish (NFE) AF: 0.446 AC: 30307 AN: 67926

Other (OTH) AF: 0.457 AC: 965 AN: 2112

Alfa AF: 0.449 Hom.: 9397

Bravo AF: 0.456

Asia WGS AF: 0.659 AC: 2290 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.30
DANN	Benign	0.76
PhyloP100		-1.1
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

Other links and lift over

dbSNP: rs8919; hg19: chr22-18213057;