chr13-108306732-A-AT

Variant names:

• chr13-108306732-A-AT
• rs11381410
• NM_006573.5:c.746-84dupT

Variant summary

Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BA1

The NM_006573.5(TNFSF13B):​c.746-84dupT 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
• Publications: 1 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 -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 rank	MANE	Protein	UniProt
TNFSF13B	NM_006573.5	c.746-84dupT		intron_variant	Intron 5 of 5	ENST00000375887.9	NP_006564.1
TNFSF13B	NM_001145645.2	c.689-84dupT		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_746-93insT		intron_variant	Intron 5 of 5	1	NM_006573.5	ENSP00000365048.3
TNFSF13B	ENST00000430559.5	c.689-94_689-93insT		intron_variant	Intron 4 of 4	1		ENSP00000389540.1
TNFSF13B	ENST00000493765.1	n.300-94_300-93insT		intron_variant	Intron 1 of 1	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

African (AFR) AF: 0.589 AC: 5399 AN: 9168

American (AMR) AF: 0.592 AC: 7860 AN: 13284

Ashkenazi Jewish (ASJ) AF: 0.530 AC: 6461 AN: 12180

East Asian (EAS) AF: 0.581 AC: 12431 AN: 21388

South Asian (SAS) AF: 0.505 AC: 18897 AN: 37448

European-Finnish (FIN) AF: 0.504 AC: 15601 AN: 30924

Middle Eastern (MID) AF: 0.594 AC: 1555 AN: 2620

European-Non Finnish (NFE) AF: 0.551 AC: 156609 AN: 284424

Other (OTH) AF: 0.546 AC: 12374 AN: 22652

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

African (AFR) AF: 0.803 AC: 32860 AN: 40914

American (AMR) AF: 0.811 AC: 12108 AN: 14936

Ashkenazi Jewish (ASJ) AF: 0.725 AC: 2501 AN: 3448

East Asian (EAS) AF: 0.780 AC: 3991 AN: 5116

South Asian (SAS) AF: 0.675 AC: 3207 AN: 4754

European-Finnish (FIN) AF: 0.622 AC: 6101 AN: 9806

Middle Eastern (MID) AF: 0.680 AC: 200 AN: 294

European-Non Finnish (NFE) AF: 0.739 AC: 49585 AN: 67138

Other (OTH) AF: 0.752 AC: 1538 AN: 2046

Alfa AF: 0.673 Hom.: 1843

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
PhyloP100		-0.43
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs11381410; hg19: chr13-108959080;