rs723858

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

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.508

Publications

8 publications found
Variant links:
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]

Genome browser will be placed here

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
TNFSF18NM_005092.4 linkc.156+1618A>T intron_variant Intron 1 of 2 ENST00000404377.5 NP_005083.3 Q9UNG2A0A0U5JXL4

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
TNFSF18ENST00000404377.5 linkc.156+1618A>T intron_variant Intron 1 of 2 1 NM_005092.4 ENSP00000385470.4 Q9UNG2
ENSG00000224000ENST00000432694.2 linkn.666-14750T>A intron_variant Intron 4 of 4 3
ENSG00000224000ENST00000717048.1 linkn.324-14750T>A intron_variant Intron 2 of 2

Frequencies

GnomAD3 genomes
AF:
0.203
AC:
30880
AN:
151976
Hom.:
4794
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.0516
Gnomad AMI
AF:
0.288
Gnomad AMR
AF:
0.299
Gnomad ASJ
AF:
0.316
Gnomad EAS
AF:
0.754
Gnomad SAS
AF:
0.460
Gnomad FIN
AF:
0.179
Gnomad MID
AF:
0.288
Gnomad NFE
AF:
0.209
Gnomad OTH
AF:
0.243
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.203
AC:
30871
AN:
152094
Hom.:
4785
Cov.:
32
AF XY:
0.210
AC XY:
15605
AN XY:
74334
show subpopulations
African (AFR)
AF:
0.0514
AC:
2134
AN:
41536
American (AMR)
AF:
0.299
AC:
4572
AN:
15272
Ashkenazi Jewish (ASJ)
AF:
0.316
AC:
1095
AN:
3468
East Asian (EAS)
AF:
0.753
AC:
3886
AN:
5160
South Asian (SAS)
AF:
0.459
AC:
2211
AN:
4816
European-Finnish (FIN)
AF:
0.179
AC:
1892
AN:
10588
Middle Eastern (MID)
AF:
0.313
AC:
92
AN:
294
European-Non Finnish (NFE)
AF:
0.209
AC:
14214
AN:
67936
Other (OTH)
AF:
0.242
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

Age Distribution

Genome Het
Genome Hom
Variant carriers
0
342
684
1026
1368
1710
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
Alfa
AF:
0.188
Hom.:
394
Bravo
AF:
0.208
Asia WGS
AF:
0.532
AC:
1848
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.85
CADD
Benign
0.56
DANN
Benign
0.47
PhyloP100
-0.51
Mutation Taster
=100/0
polymorphism (auto)

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

Other links and lift over

dbSNP: rs723858; hg19: chr1-173018263; API