NM_006573.5:c.481+3827A>G

Variant names:

• chr13-108290686-A-G
• rs2893321
• NM_006573.5:c.481+3827A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_006573.5(TNFSF13B):​c.481+3827A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.211 in 151,812 control chromosomes in the GnomAD database, including 4,048 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 0.21 (4048 hom., cov: 31)
• Consequence: TNFSF13B NM_006573.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.306
• Publications: 16 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 -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.402 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_006573.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TNFSF13B	NM_006573.5	MANE Select	c.481+3827A>G		intron	N/A	NP_006564.1	Q9Y275-1
	TNFSF13B	NM_001145645.2		c.425-12567A>G		intron	N/A	NP_001139117.1	Q9Y275-2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TNFSF13B	ENST00000375887.9	TSL:1 MANE Select	c.481+3827A>G		intron	N/A	ENSP00000365048.3	Q9Y275-1
	TNFSF13B	ENST00000430559.5	TSL:1	c.425-12567A>G		intron	N/A	ENSP00000389540.1	Q9Y275-2
	TNFSF13B	ENST00000542136.1	TSL:1	c.481+3827A>G		intron	N/A	ENSP00000445334.1	Q9Y275-3

Frequencies

GnomAD3 genomes AF: 0.211 AC: 32041 AN: 151694 Hom.: 4034 Cov.: 31

Gnomad AFR AF: 0.0983

Gnomad AMI AF: 0.265

Gnomad AMR AF: 0.350

Gnomad ASJ AF: 0.317

Gnomad EAS AF: 0.416

Gnomad SAS AF: 0.259

Gnomad FIN AF: 0.195

Gnomad MID AF: 0.288

Gnomad NFE AF: 0.225

Gnomad OTH AF: 0.243

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

GnomAD4 genome AF: 0.211 AC: 32062 AN: 151812 Hom.: 4048 Cov.: 31 AF XY: 0.212 AC XY: 15731 AN XY: 74158

African (AFR) AF: 0.0981 AC: 4068 AN: 41470

American (AMR) AF: 0.351 AC: 5355 AN: 15236

Ashkenazi Jewish (ASJ) AF: 0.317 AC: 1098 AN: 3460

East Asian (EAS) AF: 0.417 AC: 2146 AN: 5148

South Asian (SAS) AF: 0.259 AC: 1244 AN: 4806

European-Finnish (FIN) AF: 0.195 AC: 2046 AN: 10498

Middle Eastern (MID) AF: 0.299 AC: 88 AN: 294

European-Non Finnish (NFE) AF: 0.225 AC: 15266 AN: 67878

Other (OTH) AF: 0.241 AC: 509 AN: 2110

Alfa AF: 0.227 Hom.: 3118

Bravo AF: 0.220

Asia WGS AF: 0.306 AC: 1063 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.8
DANN	Benign	0.32
PhyloP100		0.31
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: rs2893321; hg19: chr13-108943034;