9-114785492-T-C
Position:
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_005118.4(TNFSF15):c.*4960A>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.748 in 152,176 control chromosomes in the GnomAD database, including 43,319 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain risk allele (no stars).
Frequency
Genomes: 𝑓 0.75 ( 43317 hom., cov: 32)
Exomes 𝑓: 0.67 ( 2 hom. )
Consequence
TNFSF15
NM_005118.4 3_prime_UTR
NM_005118.4 3_prime_UTR
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.0110
Genes affected
TNFSF15 (HGNC:11931): (TNF superfamily member 15) The protein encoded by this gene is a cytokine that belongs to the tumor necrosis factor (TNF) ligand family. This protein is abundantly expressed in endothelial cells, but is not expressed in either B or T cells. The expression of this protein is inducible by TNF and IL-1 alpha. This cytokine is a ligand for receptor TNFRSF25 and decoy receptor TNFRSF21/DR6. It can activate NF-kappaB and MAP kinases, and acts as an autocrine factor to induce apoptosis in endothelial cells. This cytokine is also found to inhibit endothelial cell proliferation, and thus may function as an angiogenesis inhibitor. Two transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Feb 2011]
Genome browser will be placed here
ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.82).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.882 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TNFSF15 | NM_005118.4 | c.*4960A>G | 3_prime_UTR_variant | 4/4 | ENST00000374045.5 | ||
TNFSF15 | NM_001204344.1 | c.*4960A>G | 3_prime_UTR_variant | 2/2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TNFSF15 | ENST00000374045.5 | c.*4960A>G | 3_prime_UTR_variant | 4/4 | 1 | NM_005118.4 | P1 |
Frequencies
GnomAD3 genomes AF: 0.747 AC: 113630AN: 152046Hom.: 43263 Cov.: 32
GnomAD3 genomes
AF:
AC:
113630
AN:
152046
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:
GnomAD4 exome AF: 0.667 AC: 8AN: 12Hom.: 2 Cov.: 0 AF XY: 0.600 AC XY: 6AN XY: 10
GnomAD4 exome
AF:
AC:
8
AN:
12
Hom.:
Cov.:
0
AF XY:
AC XY:
6
AN XY:
10
Gnomad4 NFE exome
AF:
Gnomad4 OTH exome
AF:
GnomAD4 genome AF: 0.748 AC: 113746AN: 152164Hom.: 43317 Cov.: 32 AF XY: 0.749 AC XY: 55740AN XY: 74400
GnomAD4 genome
AF:
AC:
113746
AN:
152164
Hom.:
Cov.:
32
AF XY:
AC XY:
55740
AN XY:
74400
Gnomad4 AFR
AF:
Gnomad4 AMR
AF:
Gnomad4 ASJ
AF:
Gnomad4 EAS
AF:
Gnomad4 SAS
AF:
Gnomad4 FIN
AF:
Gnomad4 NFE
AF:
Gnomad4 OTH
AF:
Alfa
AF:
Hom.:
Bravo
AF:
Asia WGS
AF:
AC:
2218
AN:
3478
ClinVar
Significance: Uncertain risk allele
Submissions summary: Other:1
Revision: no assertion criteria provided
LINK: link
Submissions by phenotype
Leprosy, susceptibility to, 1 Other:1
Uncertain risk allele, no assertion criteria provided | case-control | Centro Dermatológico Federico Lleras Acosta, Hospital Universitario Centro Dermatológico Federico Lleras Acosta | Jun 10, 2022 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
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