3-172506285-C-T
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Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The ENST00000241261.7(TNFSF10):c.*207G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.453 in 516,014 control chromosomes in the GnomAD database, including 55,064 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Genomes: 𝑓 0.50 ( 19701 hom., cov: 32)
Exomes 𝑓: 0.44 ( 35363 hom. )
Consequence
TNFSF10
ENST00000241261.7 3_prime_UTR
ENST00000241261.7 3_prime_UTR
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.252
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 -20 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.94).
BP6
Variant 3-172506285-C-T is Benign according to our data. Variant chr3-172506285-C-T is described in ClinVar as [Benign]. Clinvar id is 1237910.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.656 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
TNFSF10 | NM_003810.4 | c.*207G>A | 3_prime_UTR_variant | 5/5 | ENST00000241261.7 | NP_003801.1 | ||
TNFSF10 | NM_001190942.2 | c.*599G>A | 3_prime_UTR_variant | 3/3 | NP_001177871.1 | |||
TNFSF10 | NR_033994.2 | n.1056G>A | non_coding_transcript_exon_variant | 4/4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
TNFSF10 | ENST00000241261.7 | c.*207G>A | 3_prime_UTR_variant | 5/5 | 1 | NM_003810.4 | ENSP00000241261 | P1 | ||
TNFSF10 | ENST00000420541.6 | c.*599G>A | 3_prime_UTR_variant | 3/3 | 1 | ENSP00000389931 |
Frequencies
GnomAD3 genomes AF: 0.497 AC: 75488AN: 151908Hom.: 19684 Cov.: 32
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GnomAD4 exome AF: 0.435 AC: 158380AN: 363988Hom.: 35363 Cov.: 5 AF XY: 0.432 AC XY: 81116AN XY: 187624
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GnomAD4 genome AF: 0.497 AC: 75548AN: 152026Hom.: 19701 Cov.: 32 AF XY: 0.493 AC XY: 36619AN XY: 74316
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ClinVar
Significance: Benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not provided Benign:2
Benign, criteria provided, single submitter | not provided | Breakthrough Genomics, Breakthrough Genomics | - | - - |
Benign, criteria provided, single submitter | clinical testing | GeneDx | Nov 12, 2018 | - - |
Computational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at