rs2582869

Variant names:

• chr13-108259797-A-G
• rs2582869
• ENST00000486502.1:n.77+8481A>G

Your query was ambiguous. Multiple possible variants found:

• chr13-108259797-A-G
• chr13-108259797-A-T

Variant summary

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

The ENST00000486502.1(TNFSF13B):​n.77+8481A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.548 in 151,976 control chromosomes in the GnomAD database, including 23,760 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 0.55 (23760 hom., cov: 32)
• Consequence: TNFSF13B ENST00000486502.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.424
• Publications: 8 publications found

Genes affected

TNFSF13B (HGNC:11929): (TNF superfamily member 13b) The protein encoded by this gene is a cytokine that belongs to the tumor necrosis factor (TNF) ligand family. This cytokine is a ligand for receptors TNFRSF13B/TACI, TNFRSF17/BCMA, and TNFRSF13C/BAFFR. This cytokine is expressed in B cell lineage cells, and acts as a potent B cell activator. It has been also shown to play an important role in the proliferation and differentiation of B cells. Alternatively spliced transcript variants encoding distinct isoforms have been identified. [provided by RefSeq, Mar 2011]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.727 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TNFSF13B	ENST00000486502.1	n.77+8481A>G		intron_variant	Intron 1 of 1	5

Frequencies

GnomAD3 genomes AF: 0.548 AC: 83193 AN: 151858 Hom.: 23741 Cov.: 32

Gnomad AFR AF: 0.386

Gnomad AMI AF: 0.574

Gnomad AMR AF: 0.607

Gnomad ASJ AF: 0.678

Gnomad EAS AF: 0.745

Gnomad SAS AF: 0.506

Gnomad FIN AF: 0.544

Gnomad MID AF: 0.564

Gnomad NFE AF: 0.613

Gnomad OTH AF: 0.589

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

GnomAD4 genome AF: 0.548 AC: 83256 AN: 151976 Hom.: 23760 Cov.: 32 AF XY: 0.546 AC XY: 40544 AN XY: 74280

African (AFR) AF: 0.386 AC: 16004 AN: 41434

American (AMR) AF: 0.607 AC: 9266 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.678 AC: 2352 AN: 3470

East Asian (EAS) AF: 0.746 AC: 3852 AN: 5162

South Asian (SAS) AF: 0.507 AC: 2444 AN: 4822

European-Finnish (FIN) AF: 0.544 AC: 5746 AN: 10558

Middle Eastern (MID) AF: 0.555 AC: 162 AN: 292

European-Non Finnish (NFE) AF: 0.613 AC: 41671 AN: 67956

Other (OTH) AF: 0.586 AC: 1238 AN: 2112

Alfa AF: 0.599 Hom.: 46680

Bravo AF: 0.552

Asia WGS AF: 0.606 AC: 2105 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	3.8
DANN	Benign	0.82
PhyloP100		0.42

Splicing

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

Other links and lift over

dbSNP: rs2582869; hg19: chr13-108912145;