13-108306732-ATTT-ATTTT

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BA1

The NM_006573.5(TNFSF13B):​c.746-84dup variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.6 in 583,444 control chromosomes in the GnomAD database, including 82,608 homozygotes. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.75 ( 42461 hom., cov: 0)
Exomes 𝑓: 0.55 ( 40147 hom. )

Consequence

TNFSF13B
NM_006573.5 intron

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.431
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]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -8 ACMG points.

BA1
GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.799 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
TNFSF13BNM_006573.5 linkuse as main transcriptc.746-84dup intron_variant ENST00000375887.9
TNFSF13BNM_001145645.2 linkuse as main transcriptc.689-84dup intron_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
TNFSF13BENST00000375887.9 linkuse as main transcriptc.746-84dup intron_variant 1 NM_006573.5 P1Q9Y275-1
TNFSF13BENST00000430559.5 linkuse as main transcriptc.689-84dup intron_variant 1 Q9Y275-2
TNFSF13BENST00000493765.1 linkuse as main transcriptn.300-84dup intron_variant, non_coding_transcript_variant 2

Frequencies

GnomAD3 genomes
AF:
0.754
AC:
112513
AN:
149254
Hom.:
42423
Cov.:
0
show subpopulations
Gnomad AFR
AF:
0.803
Gnomad AMI
AF:
0.559
Gnomad AMR
AF:
0.811
Gnomad ASJ
AF:
0.725
Gnomad EAS
AF:
0.779
Gnomad SAS
AF:
0.676
Gnomad FIN
AF:
0.622
Gnomad MID
AF:
0.674
Gnomad NFE
AF:
0.739
Gnomad OTH
AF:
0.752
GnomAD4 exome
AF:
0.546
AC:
237187
AN:
434088
Hom.:
40147
AF XY:
0.544
AC XY:
124677
AN XY:
229334
show subpopulations
Gnomad4 AFR exome
AF:
0.589
Gnomad4 AMR exome
AF:
0.592
Gnomad4 ASJ exome
AF:
0.530
Gnomad4 EAS exome
AF:
0.581
Gnomad4 SAS exome
AF:
0.505
Gnomad4 FIN exome
AF:
0.504
Gnomad4 NFE exome
AF:
0.551
Gnomad4 OTH exome
AF:
0.546
GnomAD4 genome
AF:
0.754
AC:
112596
AN:
149356
Hom.:
42461
Cov.:
0
AF XY:
0.748
AC XY:
54524
AN XY:
72860
show subpopulations
Gnomad4 AFR
AF:
0.803
Gnomad4 AMR
AF:
0.811
Gnomad4 ASJ
AF:
0.725
Gnomad4 EAS
AF:
0.780
Gnomad4 SAS
AF:
0.675
Gnomad4 FIN
AF:
0.622
Gnomad4 NFE
AF:
0.739
Gnomad4 OTH
AF:
0.752

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
Details are displayed if max score is > 0.2

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs11381410; hg19: chr13-108959080; API