NM_003808.4:c.*263C>T

Variant names:

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_003808.4(TNFSF13):c.*263C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.162 in 1,596,328 control chromosomes in the GnomAD database, including 21,925 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.15 ( 1890 hom., cov: 32)

Exomes 𝑓: 0.16 ( 20035 hom. )

Consequence

TNFSF13
NM_003808.4 3_prime_UTR

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:3

Conservation

PhyloP100: 0.272

Variant links:

Genes affected

TNFSF13 (HGNC:11928): (TNF superfamily member 13) The protein encoded by this gene is a member of the tumor necrosis factor (TNF) ligand family. This protein is a ligand for TNFRSF17/BCMA, a member of the TNF receptor family. This protein and its receptor are both found to be important for B cell development. In vitro experiments suggested that this protein may be able to induce apoptosis through its interaction with other TNF receptor family proteins such as TNFRSF6/FAS and TNFRSF14/HVEM. Alternative splicing results in multiple transcript variants. Some transcripts that skip the last exon of the upstream gene (TNFSF12) and continue into the second exon of this gene have been identified; such read-through transcripts are contained in GeneID 407977, TNFSF12-TNFSF13. [provided by RefSeq, Oct 2010]

TNFSF13 links:

TNFSF12-TNFSF13 (HGNC:33537): (TNFSF12-TNFSF13 readthrough) This gene encodes a member of the tumor necrosis factor superfamily. It encodes a hybrid protein composed of the cytoplasmic and transmembrane domains of family member 12 fused to the C-terminal domain of family member 13. The hybrid protein is membrane anchored and presents the receptor-binding domain of family member 13 at the cell surface. It stimulates cycling in T- and B-lymphoma cell lines. [provided by RefSeq, Jul 2008]

TNFSF12-TNFSF13 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.78).

BP6

Variant 17-7561096-C-T is Benign according to our data. Variant chr17-7561096-C-T is described in ClinVar as [Benign]. Clinvar id is 1230540.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.171 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TNFSF13	NM_003808.4 link	c.*263C>T		3_prime_UTR_variant	Exon 6 of 6	ENST00000338784.9	NP_003799.1	O75888-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TNFSF13	ENST00000338784.9 link	c.*263C>T		3_prime_UTR_variant	Exon 6 of 6	1	NM_003808.4	ENSP00000343505.4		O75888-1
TNFSF12-TNFSF13	ENST00000293826.4 link	c.*263C>T		3_prime_UTR_variant	Exon 11 of 11	1		ENSP00000293826.4		A0A0A6YY99

Frequencies

GnomAD3 genomes

AF:

0.152

AC:

23110

AN:

151874

Hom.:

1881

Cov.:

show subpopulations

Gnomad AFR

AF:

0.174

Gnomad AMI

AF:

0.165

Gnomad AMR

AF:

0.126

Gnomad ASJ

AF:

0.187

Gnomad EAS

AF:

0.0523

Gnomad SAS

AF:

0.158

Gnomad FIN

AF:

0.0644

Gnomad MID

AF:

0.0728

Gnomad NFE

AF:

0.165

Gnomad OTH

AF:

0.144

GnomAD4 exome

AF:

0.163

AC:

235850

AN:

1444336

Hom.:

20035

Cov.:

AF XY:

0.162

AC XY:

116430

AN XY:

719328

show subpopulations

Gnomad4 AFR exome

AF:

0.175

Gnomad4 AMR exome

AF:

0.100

Gnomad4 ASJ exome

AF:

0.184

Gnomad4 EAS exome

AF:

0.0717

Gnomad4 SAS exome

AF:

0.146

Gnomad4 FIN exome

AF:

0.0774

Gnomad4 NFE exome

AF:

0.174

Gnomad4 OTH exome

AF:

0.165

GnomAD4 genome

AF:

0.152

AC:

23137

AN:

151992

Hom.:

1890

Cov.:

AF XY:

0.146

AC XY:

10876

AN XY:

74316

show subpopulations

Gnomad4 AFR

AF:

0.174

Gnomad4 AMR

AF:

0.126

Gnomad4 ASJ

AF:

0.187

Gnomad4 EAS

AF:

0.0524

Gnomad4 SAS

AF:

0.157

Gnomad4 FIN

AF:

0.0644

Gnomad4 NFE

AF:

0.164

Gnomad4 OTH

AF:

0.146

Alfa

AF:

0.161

Hom.:

2832

Bravo

AF:

0.158

Asia WGS

AF:

0.146

AC:

509

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:3

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Nov 12, 2018

GeneDx

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Breakthrough Genomics, Breakthrough Genomics

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: not provided

- -

not specified

Benign:1

Jan 24, 2024

Unidad de Genómica Garrahan, Hospital de Pediatría Garrahan

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

This variant is classified as Benign based on local population frequency. This variant was detected in 27% of patients studied by a panel of primary immunodeficiencies. Number of patients: 26. Only high quality variants are reported. -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.78

CADD

Benign

DANN

Benign

0.83

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.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over