rs1234313

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_003326.5(TNFSF4):​c.154-8539T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.714 in 152,156 control chromosomes in the GnomAD database, including 39,940 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 0.71 ( 39940 hom., cov: 33)

Consequence

TNFSF4
NM_003326.5 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.27
Variant links:
Genes affected
TNFSF4 (HGNC:11934): (TNF superfamily member 4) This gene encodes a cytokine of the tumor necrosis factor (TNF) ligand family. The encoded protein functions in T cell antigen-presenting cell (APC) interactions and mediates adhesion of activated T cells to endothelial cells. Polymorphisms in this gene have been associated with Sjogren's syndrome and systemic lupus erythematosus. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jul 2014]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.89).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.859 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
TNFSF4NM_003326.5 linkuse as main transcriptc.154-8539T>C intron_variant ENST00000281834.4

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
TNFSF4ENST00000281834.4 linkuse as main transcriptc.154-8539T>C intron_variant 1 NM_003326.5 P1P23510-1
TNFSF4ENST00000367718.5 linkuse as main transcriptc.3+8203T>C intron_variant 1 P23510-2
TNFSF4ENST00000488053.1 linkuse as main transcriptn.414+8203T>C intron_variant, non_coding_transcript_variant 3

Frequencies

GnomAD3 genomes
AF:
0.714
AC:
108604
AN:
152038
Hom.:
39886
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.866
Gnomad AMI
AF:
0.559
Gnomad AMR
AF:
0.631
Gnomad ASJ
AF:
0.742
Gnomad EAS
AF:
0.334
Gnomad SAS
AF:
0.599
Gnomad FIN
AF:
0.671
Gnomad MID
AF:
0.788
Gnomad NFE
AF:
0.685
Gnomad OTH
AF:
0.718
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.714
AC:
108711
AN:
152156
Hom.:
39940
Cov.:
33
AF XY:
0.710
AC XY:
52839
AN XY:
74382
show subpopulations
Gnomad4 AFR
AF:
0.866
Gnomad4 AMR
AF:
0.630
Gnomad4 ASJ
AF:
0.742
Gnomad4 EAS
AF:
0.334
Gnomad4 SAS
AF:
0.599
Gnomad4 FIN
AF:
0.671
Gnomad4 NFE
AF:
0.685
Gnomad4 OTH
AF:
0.720
Alfa
AF:
0.687
Hom.:
47668
Bravo
AF:
0.718
Asia WGS
AF:
0.497
AC:
1729
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.89
CADD
Benign
5.4
DANN
Benign
0.77

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: rs1234313; hg19: chr1-173166247; API