rs9514828

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 84 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=-0.82).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.468 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000486502.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TNFSF13B	ENST00000486502.1	TSL:5	n.78-1075C>T		intron	N/A

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

African (AFR) AF: 0.133 AC: 5507 AN: 41484

American (AMR) AF: 0.298 AC: 4555 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.433 AC: 1500 AN: 3462

East Asian (EAS) AF: 0.376 AC: 1933 AN: 5144

South Asian (SAS) AF: 0.484 AC: 2329 AN: 4808

European-Finnish (FIN) AF: 0.429 AC: 4528 AN: 10554

Middle Eastern (MID) AF: 0.466 AC: 136 AN: 292

European-Non Finnish (NFE) AF: 0.469 AC: 31849 AN: 67942

Other (OTH) AF: 0.371 AC: 783 AN: 2110

Alfa AF: 0.418 Hom.: 27933

Bravo AF: 0.331

Asia WGS AF: 0.399 AC: 1390 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	3.2
DANN	Benign	0.41
PhyloP100		-0.56

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs9514828;

hg19: chr13-108921373;