chr13-108269220-A-C

Variant names:

• chr13-108269220-A-C
• rs36206504
• ENST00000486502.1:n.78-880A>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The ENST00000486502.1(TNFSF13B):​n.78-880A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0186 in 152,202 control chromosomes in the GnomAD database, including 39 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 0.019 (39 hom., cov: 32)
• Consequence: TNFSF13B ENST00000486502.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.441
• Publications: 1 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=-0.83).
• BS1: Variant frequency is greater than expected in population nfe. GnomAd4 allele frequency = 0.0186 (2836/152202) while in subpopulation NFE AF = 0.0267 (1819/68012). AF 95% confidence interval is 0.0257. There are 39 homozygotes in GnomAd4. There are 1423 alleles in the male GnomAd4 subpopulation. Median coverage is 32. This position passed quality control check.
• BS2: High Homozygotes in GnomAd4 at 39 gene

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.78-880A>C		intron_variant	Intron 1 of 1	5

Frequencies

GnomAD3 genomes AF: 0.0187 AC: 2837 AN: 152084 Hom.: 39 Cov.: 32

Gnomad AFR AF: 0.00386

Gnomad AMI AF: 0.00329

Gnomad AMR AF: 0.0156

Gnomad ASJ AF: 0.0453

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.0151

Gnomad FIN AF: 0.0321

Gnomad MID AF: 0.0253

Gnomad NFE AF: 0.0267

Gnomad OTH AF: 0.0186

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

GnomAD4 genome AF: 0.0186 AC: 2836 AN: 152202 Hom.: 39 Cov.: 32 AF XY: 0.0191 AC XY: 1423 AN XY: 74402

African (AFR) AF: 0.00385 AC: 160 AN: 41526

American (AMR) AF: 0.0156 AC: 238 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.0453 AC: 157 AN: 3468

East Asian (EAS) AF: 0.00 AC: 0 AN: 5186

South Asian (SAS) AF: 0.0151 AC: 73 AN: 4820

European-Finnish (FIN) AF: 0.0321 AC: 339 AN: 10576

Middle Eastern (MID) AF: 0.0238 AC: 7 AN: 294

European-Non Finnish (NFE) AF: 0.0267 AC: 1819 AN: 68012

Other (OTH) AF: 0.0189 AC: 40 AN: 2116

Alfa AF: 0.0249 Hom.: 10

Bravo AF: 0.0163

Asia WGS AF: 0.00664 AC: 23 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	1.7
DANN	Benign	0.37
PhyloP100		0.44
PromoterAI		0.049	Neutral

Splicing

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

Other links and lift over

dbSNP: rs36206504; hg19: chr13-108921568;