dbSNP rs16972197: 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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	MANE	Protein	UniProt
TNFSF13B	NM_006573.5 link	c.-353G>C	upstream_gene_variant	ENST00000375887.9	NP_006564.1	Q9Y275-1A0A0U5J7Q1
TNFSF13B	NM_001145645.2 link	c.-353G>C	upstream_gene_variant		NP_001139117.1	Q9Y275-2
TNFSF13B	XM_047430055.1 link	c.-353G>C	upstream_gene_variant		XP_047286011.1

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL	MANE	Protein	UniProt
TNFSF13B	ENST00000486502.1 link	n.78-557G>C	intron_variant	Intron 1 of 1	5
TNFSF13B	ENST00000375887.9 link	c.-353G>C	upstream_gene_variant		1	NM_006573.5	ENSP00000365048.3	Q9Y275-1
TNFSF13B	ENST00000430559.5 link	c.-353G>C	upstream_gene_variant		1		ENSP00000389540.1	Q9Y275-2

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 v4.3

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

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over