13-108304410-C-T

Position:

• chr13-108304410-C-T

Variant summary

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

The NM_006573.5(TNFSF13B):​c.745+806C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.776 in 152,130 control chromosomes in the GnomAD database, including 46,189 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 0.78 (46189 hom., cov: 32)
• Consequence: TNFSF13B NM_006573.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.420

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]

TNFSF13B (HGNC:):

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 = 0.9 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
TNFSF13B	NM_006573.5	c.745+806C>T		intron_variant		ENST00000375887.9	NP_006564.1
TNFSF13B	NM_001145645.2	c.688+806C>T		intron_variant			NP_001139117.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
TNFSF13B	ENST00000375887.9	c.745+806C>T		intron_variant		1	NM_006573.5	ENSP00000365048.3
TNFSF13B	ENST00000430559.5	c.688+806C>T		intron_variant		1		ENSP00000389540.1
TNFSF13B	ENST00000493765.1	n.299+806C>T		intron_variant		2

Frequencies

GnomAD3 genomes AF: 0.776 AC: 117976 AN: 152012 Hom.: 46130 Cov.: 32

Gnomad AFR AF: 0.850

Gnomad AMI AF: 0.557

Gnomad AMR AF: 0.821

Gnomad ASJ AF: 0.729

Gnomad EAS AF: 0.921

Gnomad SAS AF: 0.685

Gnomad FIN AF: 0.644

Gnomad MID AF: 0.680

Gnomad NFE AF: 0.743

Gnomad OTH AF: 0.775

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.776 AC: 118089 AN: 152130 Hom.: 46189 Cov.: 32 AF XY: 0.771 AC XY: 57380 AN XY: 74376

Gnomad4 AFR AF: 0.850

Gnomad4 AMR AF: 0.821

Gnomad4 ASJ AF: 0.729

Gnomad4 EAS AF: 0.922

Gnomad4 SAS AF: 0.684

Gnomad4 FIN AF: 0.644

Gnomad4 NFE AF: 0.743

Gnomad4 OTH AF: 0.776

Alfa AF: 0.747 Hom.: 54760

Bravo AF: 0.793

Asia WGS AF: 0.790 AC: 2746 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	4.9
DANN	Benign	0.54

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: rs1224147; hg19: chr13-108956758;