rs723858
Variant names:
Your query was ambiguous. Multiple possible variants found:
Variant summary
Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_005092.4(TNFSF18):c.156+1618A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.203 in 152,094 control chromosomes in the GnomAD database, including 4,785 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 0.20 ( 4785 hom., cov: 32)
Consequence
TNFSF18
NM_005092.4 intron
NM_005092.4 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.508
Publications
8 publications found
Genes affected
TNFSF18 (HGNC:11932): (TNF superfamily member 18) 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 receptor TNFRSF18/AITR/GITR. It has been shown to modulate T lymphocyte survival in peripheral tissues. This cytokine is also found to be expressed in endothelial cells, and is thought to be important for interaction between T lymphocytes and endothelial cells. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification was made for transcript
Our verdict: Benign. The variant received -12 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.85).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.733 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
TNFSF18 | NM_005092.4 | c.156+1618A>T | intron_variant | Intron 1 of 2 | ENST00000404377.5 | NP_005083.3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
TNFSF18 | ENST00000404377.5 | c.156+1618A>T | intron_variant | Intron 1 of 2 | 1 | NM_005092.4 | ENSP00000385470.4 | |||
ENSG00000224000 | ENST00000432694.2 | n.666-14750T>A | intron_variant | Intron 4 of 4 | 3 | |||||
ENSG00000224000 | ENST00000717048.1 | n.324-14750T>A | intron_variant | Intron 2 of 2 |
Frequencies
GnomAD3 genomes AF: 0.203 AC: 30880AN: 151976Hom.: 4794 Cov.: 32 show subpopulations
GnomAD3 genomes
AF:
AC:
30880
AN:
151976
Hom.:
Cov.:
32
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome AF: 0.203 AC: 30871AN: 152094Hom.: 4785 Cov.: 32 AF XY: 0.210 AC XY: 15605AN XY: 74334 show subpopulations
GnomAD4 genome
AF:
AC:
30871
AN:
152094
Hom.:
Cov.:
32
AF XY:
AC XY:
15605
AN XY:
74334
show subpopulations
African (AFR)
AF:
AC:
2134
AN:
41536
American (AMR)
AF:
AC:
4572
AN:
15272
Ashkenazi Jewish (ASJ)
AF:
AC:
1095
AN:
3468
East Asian (EAS)
AF:
AC:
3886
AN:
5160
South Asian (SAS)
AF:
AC:
2211
AN:
4816
European-Finnish (FIN)
AF:
AC:
1892
AN:
10588
Middle Eastern (MID)
AF:
AC:
92
AN:
294
European-Non Finnish (NFE)
AF:
AC:
14214
AN:
67936
Other (OTH)
AF:
AC:
512
AN:
2112
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.501
Heterozygous variant carriers
0
1102
2204
3307
4409
5511
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Alfa
AF:
Hom.:
Bravo
AF:
Asia WGS
AF:
AC:
1848
AN:
3478
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
DANN
Benign
PhyloP100
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
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