rs6661173

Variant summary

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

The NM_003326.5(TNFSF4):​c.154-2575C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.105 in 152,138 control chromosomes in the GnomAD database, including 996 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 0.11 ( 996 hom., cov: 32)

Consequence

TNFSF4
NM_003326.5 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.130
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=-0.9).
BA1
GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.157 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
TNFSF4NM_003326.5 linkuse as main transcriptc.154-2575C>T intron_variant ENST00000281834.4 NP_003317.1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
TNFSF4ENST00000281834.4 linkuse as main transcriptc.154-2575C>T intron_variant 1 NM_003326.5 ENSP00000281834 P1P23510-1
TNFSF4ENST00000367718.5 linkuse as main transcriptc.4-2575C>T intron_variant 1 ENSP00000356691 P23510-2
TNFSF4ENST00000488053.1 linkuse as main transcriptn.415-2575C>T intron_variant, non_coding_transcript_variant 3

Frequencies

GnomAD3 genomes
AF:
0.105
AC:
15998
AN:
152020
Hom.:
993
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.155
Gnomad AMI
AF:
0.0318
Gnomad AMR
AF:
0.162
Gnomad ASJ
AF:
0.0709
Gnomad EAS
AF:
0.0759
Gnomad SAS
AF:
0.0572
Gnomad FIN
AF:
0.0596
Gnomad MID
AF:
0.0949
Gnomad NFE
AF:
0.0782
Gnomad OTH
AF:
0.0974
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.105
AC:
16017
AN:
152138
Hom.:
996
Cov.:
32
AF XY:
0.107
AC XY:
7927
AN XY:
74372
show subpopulations
Gnomad4 AFR
AF:
0.155
Gnomad4 AMR
AF:
0.162
Gnomad4 ASJ
AF:
0.0709
Gnomad4 EAS
AF:
0.0759
Gnomad4 SAS
AF:
0.0566
Gnomad4 FIN
AF:
0.0596
Gnomad4 NFE
AF:
0.0782
Gnomad4 OTH
AF:
0.0978
Alfa
AF:
0.106
Hom.:
139
Bravo
AF:
0.114
Asia WGS
AF:
0.0760
AC:
263
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.90
CADD
Benign
1.4
DANN
Benign
0.70

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: rs6661173; hg19: chr1-173160283; API