rs1131542
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Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_003810.4(TNFSF10):c.*356A>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000749 in 186,908 control chromosomes in the GnomAD database, with no homozygous occurrence. 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 0.000086 ( 0 hom., cov: 32)
Exomes 𝑓: 0.000029 ( 0 hom. )
Consequence
TNFSF10
NM_003810.4 3_prime_UTR
NM_003810.4 3_prime_UTR
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.295
Genes affected
TNFSF10 (HGNC:11925): (TNF superfamily member 10) The protein encoded by this gene is a cytokine that belongs to the tumor necrosis factor (TNF) ligand family. This protein preferentially induces apoptosis in transformed and tumor cells, but does not appear to kill normal cells although it is expressed at a significant level in most normal tissues. This protein binds to several members of TNF receptor superfamily including TNFRSF10A/TRAILR1, TNFRSF10B/TRAILR2, TNFRSF10C/TRAILR3, TNFRSF10D/TRAILR4, and possibly also to TNFRSF11B/OPG. The activity of this protein may be modulated by binding to the decoy receptors TNFRSF10C/TRAILR3, TNFRSF10D/TRAILR4, and TNFRSF11B/OPG that cannot induce apoptosis. The binding of this protein to its receptors has been shown to trigger the activation of MAPK8/JNK, caspase 8, and caspase 3. Alternatively spliced transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jul 2010]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -2 ACMG points.
PM2
?
Very rare variant in population databases, with high coverage;
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.78).
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TNFSF10 | NM_003810.4 | c.*356A>T | 3_prime_UTR_variant | 5/5 | ENST00000241261.7 | ||
TNFSF10 | NM_001190942.2 | c.*748A>T | 3_prime_UTR_variant | 3/3 | |||
TNFSF10 | NR_033994.2 | n.1205A>T | non_coding_transcript_exon_variant | 4/4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TNFSF10 | ENST00000241261.7 | c.*356A>T | 3_prime_UTR_variant | 5/5 | 1 | NM_003810.4 | P1 | ||
TNFSF10 | ENST00000420541.6 | c.*748A>T | 3_prime_UTR_variant | 3/3 | 1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000856 AC: 13AN: 151952Hom.: 0 Cov.: 32
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GnomAD4 exome AF: 0.0000286 AC: 1AN: 34956Hom.: 0 Cov.: 0 AF XY: 0.0000551 AC XY: 1AN XY: 18162
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GnomAD4 genome ? AF: 0.0000856 AC: 13AN: 151952Hom.: 0 Cov.: 32 AF XY: 0.0000808 AC XY: 6AN XY: 74218
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ClinVar
Not reported inComputational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at