rs2582869

chr13-108259797-A-Gchr13-108259797-A-T

Variant summary

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

The ENST00000486502.1(TNFSF13B):n.77+8481A>G variant causes a intron, non coding transcript 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, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.424

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

Verdict is Benign. Variant got -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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TNFSF13B	ENST00000486502.1	n.77+8481A>G		intron_variant, non_coding_transcript_variant		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

Gnomad4 AFR AF: 0.386

Gnomad4 AMR AF: 0.607

Gnomad4 ASJ AF: 0.678

Gnomad4 EAS AF: 0.746

Gnomad4 SAS AF: 0.507

Gnomad4 FIN AF: 0.544

Gnomad4 NFE AF: 0.613

Gnomad4 OTH AF: 0.586

Alfa AF: 0.606 Hom.: 37474

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2582869; hg19: chr13-108912145;