rs74932682

Variant names:

• chr22-17728062-T-A
• rs74932682
• ENST00000399777.2:n.*1484T>A

Your query was ambiguous. Multiple possible variants found:

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

Variant summary

Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BP4_Strong BS2

The ENST00000399777.2(BCL2L13):​n.*1484T>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 0.00669 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 ENST00000399777.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0150
• Publications: 1 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 -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 rank	MANE	Protein	UniProt
BCL2L13	NM_015367.4	c.*528T>A		3_prime_UTR_variant	Exon 7 of 7	ENST00000317582.10	NP_056182.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
BCL2L13	ENST00000317582.10	c.*528T>A		3_prime_UTR_variant	Exon 7 of 7	1	NM_015367.4	ENSP00000318883.5

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

African (AFR) AF: 0.00 AC: 0 AN: 96

American (AMR) AF: 0.00483 AC: 10 AN: 2072

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 44

East Asian (EAS) AF: 0.00 AC: 0 AN: 532

South Asian (SAS) AF: 0.00 AC: 0 AN: 1028

European-Finnish (FIN) AF: 0.0179 AC: 1 AN: 56

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 2

European-Non Finnish (NFE) AF: 0.00889 AC: 37 AN: 4162

Other (OTH) AF: 0.0103 AC: 3 AN: 292

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

African (AFR) AF: 0.00130 AC: 54 AN: 41560

American (AMR) AF: 0.00235 AC: 36 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.00403 AC: 14 AN: 3472

East Asian (EAS) AF: 0.00 AC: 0 AN: 5172

South Asian (SAS) AF: 0.00 AC: 0 AN: 4828

European-Finnish (FIN) AF: 0.0306 AC: 325 AN: 10606

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 294

European-Non Finnish (NFE) AF: 0.00853 AC: 580 AN: 68032

Other (OTH) AF: 0.00473 AC: 10 AN: 2114

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
PhyloP100		0.015
Mutation Taster		=100/0	polymorphism

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

Other links and lift over

dbSNP: rs74932682; hg19: chr22-18210828;