13-108306732-ATTT-ATTTTT

Variant names:

• chr13-108306732-A-ATT
• rs11381410
• NM_006573.5:c.746-85_746-84dupTT

Variant summary

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

The NM_006573.5(TNFSF13B):​c.746-85_746-84dupTT variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.038 in 566,498 control chromosomes in the GnomAD database, including 102 homozygotes. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.0086 (63 hom., cov: 0)
  • Exomes 𝑓: 0.049 (39 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 (EAS) allele frequency at 95% confidence interval = 0.131 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TNFSF13B	NM_006573.5	c.746-85_746-84dupTT		intron_variant	Intron 5 of 5	ENST00000375887.9	NP_006564.1
TNFSF13B	NM_001145645.2	c.689-85_689-84dupTT		intron_variant	Intron 4 of 4		NP_001139117.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TNFSF13B	ENST00000375887.9	c.746-94_746-93insTT		intron_variant	Intron 5 of 5	1	NM_006573.5	ENSP00000365048.3
TNFSF13B	ENST00000430559.5	c.689-94_689-93insTT		intron_variant	Intron 4 of 4	1		ENSP00000389540.1
TNFSF13B	ENST00000493765.1	n.300-94_300-93insTT		intron_variant	Intron 1 of 1	2

Frequencies

GnomAD3 genomes AF: 0.00862 AC: 1287 AN: 149280 Hom.: 63 Cov.: 0

Gnomad AFR AF: 0.00179

Gnomad AMI AF: 0.00332

Gnomad AMR AF: 0.00362

Gnomad ASJ AF: 0.00348

Gnomad EAS AF: 0.140

Gnomad SAS AF: 0.0105

Gnomad FIN AF: 0.0135

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00340

Gnomad OTH AF: 0.00837

GnomAD4 exome AF: 0.0485 AC: 20231 AN: 417116 Hom.: 39 AF XY: 0.0481 AC XY: 10599 AN XY: 220346

Gnomad4 AFR exome AF: 0.0531

Gnomad4 AMR exome AF: 0.0585

Gnomad4 ASJ exome AF: 0.0426

Gnomad4 EAS exome AF: 0.161

Gnomad4 SAS exome AF: 0.0399

Gnomad4 FIN exome AF: 0.0385

Gnomad4 NFE exome AF: 0.0420

Gnomad4 OTH exome AF: 0.0528

GnomAD4 genome AF: 0.00861 AC: 1286 AN: 149382 Hom.: 63 Cov.: 0 AF XY: 0.00988 AC XY: 720 AN XY: 72878

Gnomad4 AFR AF: 0.00178

Gnomad4 AMR AF: 0.00361

Gnomad4 ASJ AF: 0.00348

Gnomad4 EAS AF: 0.140

Gnomad4 SAS AF: 0.0103

Gnomad4 FIN AF: 0.0135

Gnomad4 NFE AF: 0.00340

Gnomad4 OTH AF: 0.00927

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Splicing

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;