chr3-172506136-T-G
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_003810.4(TNFSF10):c.*356A>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.687 in 186,856 control chromosomes in the GnomAD database, including 44,728 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 0.69 ( 37042 hom., cov: 32)
Exomes 𝑓: 0.65 ( 7686 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 Benign. Variant got -12 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.8).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.768 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TNFSF10 | NM_003810.4 | c.*356A>C | 3_prime_UTR_variant | 5/5 | ENST00000241261.7 | ||
TNFSF10 | NM_001190942.2 | c.*748A>C | 3_prime_UTR_variant | 3/3 | |||
TNFSF10 | NR_033994.2 | n.1205A>C | non_coding_transcript_exon_variant | 4/4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TNFSF10 | ENST00000241261.7 | c.*356A>C | 3_prime_UTR_variant | 5/5 | 1 | NM_003810.4 | P1 | ||
TNFSF10 | ENST00000420541.6 | c.*748A>C | 3_prime_UTR_variant | 3/3 | 1 |
Frequencies
GnomAD3 genomes AF: 0.695 AC: 105500AN: 151902Hom.: 37027 Cov.: 32
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GnomAD4 exome AF: 0.654 AC: 22783AN: 34836Hom.: 7686 Cov.: 0 AF XY: 0.652 AC XY: 11804AN XY: 18092
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GnomAD4 genome AF: 0.694 AC: 105563AN: 152020Hom.: 37042 Cov.: 32 AF XY: 0.692 AC XY: 51399AN XY: 74322
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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