rs9514827

Variant names:

• chr13-108267055-T-C
• rs9514827
• ENST00000486502.1:n.78-3045T>C

Your query was ambiguous. Multiple possible variants found:

• chr13-108267055-T-C
• chr13-108267055-T-G

Variant summary

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

The ENST00000486502.1(TNFSF13B):​n.78-3045T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.243 in 152,152 control chromosomes in the GnomAD database, including 5,466 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 0.24 (5466 hom., cov: 32)
• Consequence: TNFSF13B ENST00000486502.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.184

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=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.416 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.78-3045T>C		intron_variant	Intron 1 of 1	5

Frequencies

GnomAD3 genomes AF: 0.243 AC: 36995 AN: 152034 Hom.: 5468 Cov.: 32

Gnomad AFR AF: 0.0839

Gnomad AMI AF: 0.351

Gnomad AMR AF: 0.208

Gnomad ASJ AF: 0.313

Gnomad EAS AF: 0.432

Gnomad SAS AF: 0.324

Gnomad FIN AF: 0.348

Gnomad MID AF: 0.291

Gnomad NFE AF: 0.307

Gnomad OTH AF: 0.257

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

GnomAD4 genome AF: 0.243 AC: 37010 AN: 152152 Hom.: 5466 Cov.: 32 AF XY: 0.248 AC XY: 18474 AN XY: 74370

Gnomad4 AFR AF: 0.0843

Gnomad4 AMR AF: 0.208

Gnomad4 ASJ AF: 0.313

Gnomad4 EAS AF: 0.431

Gnomad4 SAS AF: 0.323

Gnomad4 FIN AF: 0.348

Gnomad4 NFE AF: 0.307

Gnomad4 OTH AF: 0.254

Alfa AF: 0.284 Hom.: 9061

Bravo AF: 0.227

Asia WGS AF: 0.352 AC: 1225 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	4.0
DANN	Benign	0.48

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9514827; hg19: chr13-108919403;