rs1041569

chr13-108267195-T-Achr13-108267195-T-C

Variant summary

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

The ENST00000486502.1(TNFSF13B):n.78-2905T>A 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 0.82 in 152,140 control chromosomes in the GnomAD database, including 51,366 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 0.82 (51365 hom., cov: 32)
  • Exomes 𝑓: 0.75 (1 hom.)
• Consequence: TNFSF13B ENST00000486502.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.378

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=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.864 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.78-2905T>A		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.820 AC: 124697 AN: 152018 Hom.: 51300 Cov.: 32

Gnomad AFR AF: 0.832

Gnomad AMI AF: 0.860

Gnomad AMR AF: 0.852

Gnomad ASJ AF: 0.829

Gnomad EAS AF: 0.885

Gnomad SAS AF: 0.645

Gnomad FIN AF: 0.897

Gnomad MID AF: 0.755

Gnomad NFE AF: 0.801

Gnomad OTH AF: 0.811

GnomAD4 exome AF: 0.750 AC: 3 AN: 4 Hom.: 1 AF XY: 0.750 AC XY: 3 AN XY: 4

Gnomad4 NFE exome AF: 0.750

GnomAD4 genome AF: 0.820 AC: 124818 AN: 152136 Hom.: 51365 Cov.: 32 AF XY: 0.823 AC XY: 61225 AN XY: 74364

Gnomad4 AFR AF: 0.832

Gnomad4 AMR AF: 0.852

Gnomad4 ASJ AF: 0.829

Gnomad4 EAS AF: 0.885

Gnomad4 SAS AF: 0.646

Gnomad4 FIN AF: 0.897

Gnomad4 NFE AF: 0.801

Gnomad4 OTH AF: 0.811

Alfa AF: 0.820 Hom.: 5977

Bravo AF: 0.825

Asia WGS AF: 0.768 AC: 2672 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
Cadd	Benign	0.70
Dann	Benign	0.34

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1041569; hg19: chr13-108919543;