Genetic Variant TNFSF13B:n.78-557G>C (chr13-108269543-G-C) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000486502.1(TNFSF13B):n.78-557G>C variant causes a intron 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

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.990

Publications

3 publications found

Variant links:

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]

TNFSF13B links:

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ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -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.

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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TNFSF13B	NM_006573.5	MANE Select	c.-353G>C		upstream_gene	N/A	NP_006564.1
	TNFSF13B	NM_001145645.2		c.-353G>C		upstream_gene	N/A	NP_001139117.1

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
TNFSF13B	ENST00000486502.1	TSL:5	n.78-557G>C	intron	N/A
TNFSF13B	ENST00000375887.9	TSL:1 MANE Select	c.-353G>C	upstream_gene	N/A	ENSP00000365048.3
TNFSF13B	ENST00000430559.5	TSL:1	c.-353G>C	upstream_gene	N/A	ENSP00000389540.1

Frequencies

GnomAD3 genomes

AF:

0.0303

AC:

4609

AN:

152084

Hom.:

243

Cov.:

show subpopulations

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.:

AF XY:

0.0217

AC XY:

374

AN XY:

17202

show subpopulations

African (AFR)

AF:

0.0324

AC:

AN:

864

American (AMR)

AF:

0.159

AC:

299

AN:

1876

Ashkenazi Jewish (ASJ)

AF:

0.00204

AC:

AN:

982

East Asian (EAS)

AF:

0.121

AC:

163

AN:

1344

South Asian (SAS)

AF:

0.0169

AC:

AN:

3604

European-Finnish (FIN)

AF:

0.00385

AC:

AN:

1298

Middle Eastern (MID)

AF:

0.00

AC:

AN:

120

European-Non Finnish (NFE)

AF:

0.00705

AC:

147

AN:

20842

Other (OTH)

AF:

0.0225

AC:

AN:

2002

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

107

143

179

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

100

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.0304

AC:

4621

AN:

152202

Hom.:

245

Cov.:

AF XY:

0.0321

AC XY:

2389

AN XY:

74402

show subpopulations

African (AFR)

AF:

0.0282

AC:

1170

AN:

41530

American (AMR)

AF:

0.136

AC:

2085

AN:

15286

Ashkenazi Jewish (ASJ)

AF:

0.000865

AC:

AN:

3470

East Asian (EAS)

AF:

0.121

AC:

623

AN:

5152

South Asian (SAS)

AF:

0.0246

AC:

119

AN:

4830

European-Finnish (FIN)

AF:

0.00330

AC:

AN:

10602

Middle Eastern (MID)

AF:

0.00

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.00762

AC:

518

AN:

68014

Other (OTH)

AF:

0.0322

AC:

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

215

429

644

858

1073

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

138

184

230

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.0190

Hom.:

Bravo

AF:

0.0449

Asia WGS

AF:

0.0730

AC:

253

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.84

CADD

Benign

0.34

(source)

DANN

Benign

0.42

PhyloP100

-0.99

PromoterAI

0.032

Neutral

(source)

Splicing

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

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over