13-108306732-A-AT

Position:

• chr13-108306732-A-AT

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BA1

The NM_006573.5(TNFSF13B):​c.746-84dup variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.6 in 583,444 control chromosomes in the GnomAD database, including 82,608 homozygotes. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.75 (42461 hom., cov: 0)
  • Exomes 𝑓: 0.55 (40147 hom.)
• Consequence: TNFSF13B NM_006573.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.431

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 -8 ACMG points.

• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.799 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TNFSF13B	NM_006573.5	c.746-84dup		intron_variant		ENST00000375887.9
TNFSF13B	NM_001145645.2	c.689-84dup		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TNFSF13B	ENST00000375887.9	c.746-84dup		intron_variant		1	NM_006573.5	P1
TNFSF13B	ENST00000430559.5	c.689-84dup		intron_variant		1
TNFSF13B	ENST00000493765.1	n.300-84dup		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.754 AC: 112513 AN: 149254 Hom.: 42423 Cov.: 0

Gnomad AFR AF: 0.803

Gnomad AMI AF: 0.559

Gnomad AMR AF: 0.811

Gnomad ASJ AF: 0.725

Gnomad EAS AF: 0.779

Gnomad SAS AF: 0.676

Gnomad FIN AF: 0.622

Gnomad MID AF: 0.674

Gnomad NFE AF: 0.739

Gnomad OTH AF: 0.752

GnomAD4 exome AF: 0.546 AC: 237187 AN: 434088 Hom.: 40147 AF XY: 0.544 AC XY: 124677 AN XY: 229334

Gnomad4 AFR exome AF: 0.589

Gnomad4 AMR exome AF: 0.592

Gnomad4 ASJ exome AF: 0.530

Gnomad4 EAS exome AF: 0.581

Gnomad4 SAS exome AF: 0.505

Gnomad4 FIN exome AF: 0.504

Gnomad4 NFE exome AF: 0.551

Gnomad4 OTH exome AF: 0.546

GnomAD4 genome AF: 0.754 AC: 112596 AN: 149356 Hom.: 42461 Cov.: 0 AF XY: 0.748 AC XY: 54524 AN XY: 72860

Gnomad4 AFR AF: 0.803

Gnomad4 AMR AF: 0.811

Gnomad4 ASJ AF: 0.725

Gnomad4 EAS AF: 0.780

Gnomad4 SAS AF: 0.675

Gnomad4 FIN AF: 0.622

Gnomad4 NFE AF: 0.739

Gnomad4 OTH AF: 0.752

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs11381410; hg19: chr13-108959080;