13-108267195-T-A

Variant names:

• chr13-108267195-T-A
• rs1041569
• ENST00000486502.1:n.78-2905T>A

Variant summary

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

The ENST00000486502.1(TNFSF13B):​n.78-2905T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.82 in 152,140 control chromosomes in the GnomAD database, including 51,366 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 0.82 (51365 hom., cov: 32)
  • Exomes 𝑓: 0.75 (1 hom.)
• Consequence: TNFSF13B ENST00000486502.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.378
• Publications: 24 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]

ENSG00000277246 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.864 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000486502.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TNFSF13B	ENST00000486502.1	TSL:5	n.78-2905T>A		intron	N/A
	ENSG00000277246	ENST00000619612.1	TSL:6	n.-125T>A		upstream_gene	N/A

Frequencies

GnomAD3 genomes AF: 0.820 AC: 124697 AN: 152018 Hom.: 51300 Cov.: 32

Gnomad AFR AF: 0.832

Gnomad AMI AF: 0.860

Gnomad AMR AF: 0.852

Gnomad ASJ AF: 0.829

Gnomad EAS AF: 0.885

Gnomad SAS AF: 0.645

Gnomad FIN AF: 0.897

Gnomad MID AF: 0.755

Gnomad NFE AF: 0.801

Gnomad OTH AF: 0.811

GnomAD4 exome AF: 0.750 AC: 3 AN: 4 Hom.: 1 AF XY: 0.750 AC XY: 3 AN XY: 4

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.750 AC: 3 AN: 4

Other (OTH) AC: 0 AN: 0

GnomAD4 genome AF: 0.820 AC: 124818 AN: 152136 Hom.: 51365 Cov.: 32 AF XY: 0.823 AC XY: 61225 AN XY: 74364

African (AFR) AF: 0.832 AC: 34526 AN: 41488

American (AMR) AF: 0.852 AC: 13028 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.829 AC: 2876 AN: 3470

East Asian (EAS) AF: 0.885 AC: 4569 AN: 5162

South Asian (SAS) AF: 0.646 AC: 3114 AN: 4824

European-Finnish (FIN) AF: 0.897 AC: 9501 AN: 10596

Middle Eastern (MID) AF: 0.757 AC: 221 AN: 292

European-Non Finnish (NFE) AF: 0.801 AC: 54487 AN: 67994

Other (OTH) AF: 0.811 AC: 1715 AN: 2114

Alfa AF: 0.820 Hom.: 5977

Bravo AF: 0.825

Asia WGS AF: 0.768 AC: 2672 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.70
DANN	Benign	0.34
PhyloP100		-0.38

Splicing

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

Other links and lift over

dbSNP: rs1041569; hg19: chr13-108919543;