chr13-108269025-C-T

Variant names:

• chr13-108269025-C-T
• rs9514828
• ENST00000486502.1:n.78-1075C>T

Variant summary

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

The ENST00000486502.1(TNFSF13B):​n.78-1075C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.352 in 151,982 control chromosomes in the GnomAD database, including 11,214 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 0.35 (11214 hom., cov: 32)
• Consequence: TNFSF13B ENST00000486502.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.562

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=-0.82).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.468 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.78-1075C>T		intron_variant	Intron 1 of 1	5

Frequencies

GnomAD3 genomes AF: 0.353 AC: 53583 AN: 151864 Hom.: 11220 Cov.: 32

Gnomad AFR AF: 0.133

Gnomad AMI AF: 0.491

Gnomad AMR AF: 0.299

Gnomad ASJ AF: 0.433

Gnomad EAS AF: 0.376

Gnomad SAS AF: 0.484

Gnomad FIN AF: 0.429

Gnomad MID AF: 0.472

Gnomad NFE AF: 0.469

Gnomad OTH AF: 0.377

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

GnomAD4 genome AF: 0.352 AC: 53568 AN: 151982 Hom.: 11214 Cov.: 32 AF XY: 0.354 AC XY: 26274 AN XY: 74290

Gnomad4 AFR AF: 0.133

Gnomad4 AMR AF: 0.298

Gnomad4 ASJ AF: 0.433

Gnomad4 EAS AF: 0.376

Gnomad4 SAS AF: 0.484

Gnomad4 FIN AF: 0.429

Gnomad4 NFE AF: 0.469

Gnomad4 OTH AF: 0.371

Alfa AF: 0.446 Hom.: 21148

Bravo AF: 0.331

Asia WGS AF: 0.399 AC: 1390 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	3.2
DANN	Benign	0.41

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9514828; hg19: chr13-108921373;