rs16972217

Variant names:

• chr13-108283099-C-T
• rs16972217
• NM_006573.5:c.425-3704C>T

Variant summary

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

The ENST00000375887.9(TNFSF13B):​c.425-3704C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.216 in 152,168 control chromosomes in the GnomAD database, including 4,229 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 0.22 (4229 hom., cov: 33)
• Consequence: TNFSF13B ENST00000375887.9 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.372
• Publications: 5 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=-1.0).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.422 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000375887.9. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TNFSF13B	NM_006573.5	MANE Select	c.425-3704C>T		intron	N/A	NP_006564.1
	TNFSF13B	NM_001145645.2		c.424+12675C>T		intron	N/A	NP_001139117.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TNFSF13B	ENST00000375887.9	TSL:1 MANE Select	c.425-3704C>T		intron	N/A	ENSP00000365048.3
	TNFSF13B	ENST00000430559.5	TSL:1	c.424+12675C>T		intron	N/A	ENSP00000389540.1
	TNFSF13B	ENST00000542136.1	TSL:1	c.425-3704C>T		intron	N/A	ENSP00000445334.1

Frequencies

GnomAD3 genomes AF: 0.216 AC: 32779 AN: 152050 Hom.: 4215 Cov.: 33

Gnomad AFR AF: 0.0994

Gnomad AMI AF: 0.265

Gnomad AMR AF: 0.357

Gnomad ASJ AF: 0.322

Gnomad EAS AF: 0.436

Gnomad SAS AF: 0.258

Gnomad FIN AF: 0.197

Gnomad MID AF: 0.288

Gnomad NFE AF: 0.230

Gnomad OTH AF: 0.253

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

GnomAD4 genome AF: 0.216 AC: 32800 AN: 152168 Hom.: 4229 Cov.: 33 AF XY: 0.216 AC XY: 16097 AN XY: 74382

African (AFR) AF: 0.0992 AC: 4120 AN: 41536

American (AMR) AF: 0.358 AC: 5469 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.322 AC: 1117 AN: 3472

East Asian (EAS) AF: 0.437 AC: 2254 AN: 5160

South Asian (SAS) AF: 0.257 AC: 1243 AN: 4828

European-Finnish (FIN) AF: 0.197 AC: 2081 AN: 10586

Middle Eastern (MID) AF: 0.296 AC: 87 AN: 294

European-Non Finnish (NFE) AF: 0.230 AC: 15655 AN: 67996

Other (OTH) AF: 0.252 AC: 533 AN: 2114

Alfa AF: 0.235 Hom.: 16344

Bravo AF: 0.226

Asia WGS AF: 0.310 AC: 1079 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.95
DANN	Benign	0.40
PhyloP100		-0.37
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: rs16972217; hg19: chr13-108935447;