rs16972197

Positions:

• chr13-108269543-G-C

Variant summary

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

The ENST00000486502.1(TNFSF13B):​n.78-557G>C variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.029 in 185,134 control chromosomes in the GnomAD database, including 286 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 0.030 (245 hom., cov: 32)
  • Exomes 𝑓: 0.023 (41 hom.)
• Consequence: TNFSF13B ENST00000486502.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.990

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 -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.132 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
TNFSF13B	ENST00000486502.1	n.78-557G>C		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.0303 AC: 4609 AN: 152084 Hom.: 243 Cov.: 32

Gnomad AFR AF: 0.0281

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.136

Gnomad ASJ AF: 0.000865

Gnomad EAS AF: 0.120

Gnomad SAS AF: 0.0244

Gnomad FIN AF: 0.00330

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00762

Gnomad OTH AF: 0.0325

GnomAD4 exome AF: 0.0228 AC: 750 AN: 32932 Hom.: 41 AF XY: 0.0217 AC XY: 374 AN XY: 17202

Gnomad4 AFR exome AF: 0.0324

Gnomad4 AMR exome AF: 0.159

Gnomad4 ASJ exome AF: 0.00204

Gnomad4 EAS exome AF: 0.121

Gnomad4 SAS exome AF: 0.0169

Gnomad4 FIN exome AF: 0.00385

Gnomad4 NFE exome AF: 0.00705

Gnomad4 OTH exome AF: 0.0225

GnomAD4 genome AF: 0.0304 AC: 4621 AN: 152202 Hom.: 245 Cov.: 32 AF XY: 0.0321 AC XY: 2389 AN XY: 74402

Gnomad4 AFR AF: 0.0282

Gnomad4 AMR AF: 0.136

Gnomad4 ASJ AF: 0.000865

Gnomad4 EAS AF: 0.121

Gnomad4 SAS AF: 0.0246

Gnomad4 FIN AF: 0.00330

Gnomad4 NFE AF: 0.00762

Gnomad4 OTH AF: 0.0322

Alfa AF: 0.0190 Hom.: 27

Bravo AF: 0.0449

Asia WGS AF: 0.0730 AC: 253 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	0.34
DANN	Benign	0.42

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs16972197; hg19: chr13-108921891;