Genetic Variant TNFSF13B:c.746-86_746-84dupTTT (chr13-108306732-A-ATTT) – ACMG Classification: Uncertain_significance (0 pts)

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 0P and 0B.

The NM_006573.5(TNFSF13B):c.746-86_746-84dupTTT variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000259 in 585,938 control chromosomes in the GnomAD database, with no homozygous occurrence. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.000040 ( 0 hom., cov: 0)

Exomes 𝑓: 0.00033 ( 0 hom. )

Consequence

TNFSF13B
NM_006573.5 intron

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.431

Publications

1 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: Uncertain_significance. The variant received 0 ACMG points.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TNFSF13B	NM_006573.5 link	c.746-86_746-84dupTTT		intron_variant	Intron 5 of 5	ENST00000375887.9	NP_006564.1	Q9Y275-1A0A0U5J7Q1
TNFSF13B	NM_001145645.2 link	c.689-86_689-84dupTTT		intron_variant	Intron 4 of 4		NP_001139117.1	Q9Y275-2

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL	MANE	Protein	UniProt
TNFSF13B	ENST00000375887.9 link	c.746-94_746-93insTTT	intron_variant	Intron 5 of 5	1	NM_006573.5	ENSP00000365048.3	Q9Y275-1
TNFSF13B	ENST00000430559.5 link	c.689-94_689-93insTTT	intron_variant	Intron 4 of 4	1		ENSP00000389540.1	Q9Y275-2
TNFSF13B	ENST00000493765.1 link	n.300-94_300-93insTTT	intron_variant	Intron 1 of 1	2

Frequencies

GnomAD3 genomes

AF:

0.0000402

AC:

AN:

149330

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.000973

Gnomad SAS

AF:

0.000210

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.00

Gnomad OTH

AF:

0.00

GnomAD4 exome

AF:

0.000334

AC:

146

AN:

436506

Hom.:

AF XY:

0.000381

AC XY:

AN XY:

230684

show subpopulations

⚠️ The allele balance in gnomAD version 4 Exomes is significantly skewed from the expected value of 0.5.

African (AFR)

AF:

0.000326

AC:

AN:

9198

American (AMR)

AF:

0.000150

AC:

AN:

13312

Ashkenazi Jewish (ASJ)

AF:

0.000245

AC:

AN:

12260

East Asian (EAS)

AF:

0.00289

AC:

AN:

21454

South Asian (SAS)

AF:

0.000583

AC:

AN:

37712

European-Finnish (FIN)

AF:

0.000160

AC:

AN:

31176

Middle Eastern (MID)

AF:

0.00

AC:

AN:

2630

European-Non Finnish (NFE)

AF:

0.000143

AC:

AN:

285978

Other (OTH)

AF:

0.000351

AC:

AN:

22786

⚠️ The allele balance in gnomAD4 Exomes is highly skewed from 0.5 (p-value = 0), which strongly suggests a high chance of mosaicism in these individuals.

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.305

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Variant carriers

<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:

0.0000402

AC:

AN:

149432

Hom.:

Cov.:

AF XY:

0.0000411

AC XY:

AN XY:

72910

show subpopulations

African (AFR)

AF:

0.00

AC:

AN:

40932

American (AMR)

AF:

0.00

AC:

AN:

14948

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

3448

East Asian (EAS)

AF:

0.000975

AC:

AN:

5126

South Asian (SAS)

AF:

0.000210

AC:

AN:

4756

European-Finnish (FIN)

AF:

0.00

AC:

AN:

9822

Middle Eastern (MID)

AF:

0.00

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.00

AC:

AN:

67152

Other (OTH)

AF:

0.00

AC:

AN:

2050

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.492

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Variant carriers

<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:

0.00

Hom.:

1843

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

PhyloP100

-0.43

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