rs1224177

Variant names:

• chr13-108261008-G-T
• rs1224177
• ENST00000486502.1:n.78-9092G>T

Variant summary

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

The ENST00000486502.1(TNFSF13B):​n.78-9092G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.318 in 151,626 control chromosomes in the GnomAD database, including 7,894 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 0.32 (7894 hom., cov: 32)
• Consequence: TNFSF13B ENST00000486502.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.129
• Publications: 4 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=-1.03).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.39 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TNFSF13B	ENST00000486502.1	n.78-9092G>T		intron_variant	Intron 1 of 1	5

Frequencies

GnomAD3 genomes AF: 0.318 AC: 48163 AN: 151508 Hom.: 7887 Cov.: 32

Gnomad AFR AF: 0.286

Gnomad AMI AF: 0.249

Gnomad AMR AF: 0.399

Gnomad ASJ AF: 0.386

Gnomad EAS AF: 0.323

Gnomad SAS AF: 0.200

Gnomad FIN AF: 0.351

Gnomad MID AF: 0.280

Gnomad NFE AF: 0.319

Gnomad OTH AF: 0.334

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

GnomAD4 genome AF: 0.318 AC: 48209 AN: 151626 Hom.: 7894 Cov.: 32 AF XY: 0.318 AC XY: 23540 AN XY: 74084

African (AFR) AF: 0.286 AC: 11824 AN: 41336

American (AMR) AF: 0.399 AC: 6084 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.386 AC: 1340 AN: 3468

East Asian (EAS) AF: 0.323 AC: 1670 AN: 5166

South Asian (SAS) AF: 0.201 AC: 967 AN: 4816

European-Finnish (FIN) AF: 0.351 AC: 3654 AN: 10402

Middle Eastern (MID) AF: 0.274 AC: 80 AN: 292

European-Non Finnish (NFE) AF: 0.319 AC: 21656 AN: 67864

Other (OTH) AF: 0.336 AC: 707 AN: 2104

Alfa AF: 0.332 Hom.: 1051

Bravo AF: 0.325

Asia WGS AF: 0.291 AC: 1005 AN: 3448

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.77
DANN	Benign	0.20
PhyloP100		-0.13

Splicing

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

Other links and lift over

dbSNP: rs1224177; hg19: chr13-108913356;