1-7920936-T-A
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Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6_Moderate
The NM_001561.6(TNFRSF9):c.680-13A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000107 in 1,519,632 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.000033 ( 0 hom., cov: 31)
Exomes 𝑓: 0.00011 ( 0 hom. )
Consequence
TNFRSF9
NM_001561.6 intron
NM_001561.6 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.851
Genes affected
TNFRSF9 (HGNC:11924): (TNF receptor superfamily member 9) The protein encoded by this gene is a member of the TNF-receptor superfamily. This receptor contributes to the clonal expansion, survival, and development of T cells. It can also induce proliferation in peripheral monocytes, enhance T cell apoptosis induced by TCR/CD3 triggered activation, and regulate CD28 co-stimulation to promote Th1 cell responses. The expression of this receptor is induced by lymphocyte activation. TRAF adaptor proteins have been shown to bind to this receptor and transduce the signals leading to activation of NF-kappaB. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -4 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.89).
BP6
Variant 1-7920936-T-A is Benign according to our data. Variant chr1-7920936-T-A is described in ClinVar as [Likely_benign]. Clinvar id is 1610364.Status of the report is criteria_provided_single_submitter, 1 stars.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
TNFRSF9 | NM_001561.6 | c.680-13A>T | intron_variant | ENST00000377507.8 | NP_001552.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
TNFRSF9 | ENST00000377507.8 | c.680-13A>T | intron_variant | 1 | NM_001561.6 | ENSP00000366729.3 |
Frequencies
GnomAD3 genomes AF: 0.0000329 AC: 5AN: 151984Hom.: 0 Cov.: 31
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GnomAD4 exome AF: 0.000115 AC: 157AN: 1367648Hom.: 0 Cov.: 26 AF XY: 0.000115 AC XY: 79AN XY: 684364
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GnomAD4 genome AF: 0.0000329 AC: 5AN: 151984Hom.: 0 Cov.: 31 AF XY: 0.0000404 AC XY: 3AN XY: 74246
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Aug 15, 2021 | - - |
Computational scores
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Benign
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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