chr9-114930064-G-A
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_001244.4(TNFSF8):c.195+45C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.077 in 1,395,648 control chromosomes in the GnomAD database, including 14,214 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 0.21 ( 6922 hom., cov: 30)
Exomes 𝑓: 0.061 ( 7292 hom. )
Consequence
TNFSF8
NM_001244.4 intron
NM_001244.4 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.404
Genes affected
TNFSF8 (HGNC:11938): (TNF superfamily member 8) The protein encoded by this gene is a cytokine that belongs to the tumor necrosis factor (TNF) ligand family. This cytokine is a ligand for TNFRSF8/CD30, which is a cell surface antigen and a marker for Hodgkin lymphoma and related hematologic malignancies. The engagement of this cytokine expressed on B cell surface plays an inhibitory role in modulating Ig class switch. This cytokine was shown to enhance cell proliferation of some lymphoma cell lines, while to induce cell death and reduce cell proliferation of other lymphoma cell lines. The pleiotropic biologic activities of this cytokine on different CD30+ lymphoma cell lines may play a pathophysiologic role in Hodgkin's and some non-Hodgkin's lymphomas. Two transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Nov 2011]
DELEC1 (HGNC:23658): (deleted in esophageal cancer 1) The function of this gene is not known. This gene is located in a region commonly deleted in esophageal squamous cell carcinomas. Gene expression is reduced or absent in these carcinomas and thus this is a candidate tumor suppressor gene for esophageal squamous cell carcinomas. [provided by RefSeq, Jul 2008]
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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=-0.83).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.543 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TNFSF8 | NM_001244.4 | c.195+45C>T | intron_variant | ENST00000223795.3 | |||
TNFSF8 | NM_001252290.1 | c.195+45C>T | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TNFSF8 | ENST00000223795.3 | c.195+45C>T | intron_variant | 1 | NM_001244.4 | P1 | |||
TNFSF8 | ENST00000618336.4 | c.195+45C>T | intron_variant | 3 | |||||
DELEC1 | ENST00000648852.1 | n.198+8466G>A | intron_variant, non_coding_transcript_variant | ||||||
DELEC1 | ENST00000649565.1 | n.226-39520G>A | intron_variant, non_coding_transcript_variant |
Frequencies
GnomAD3 genomes AF: 0.206 AC: 31251AN: 151432Hom.: 6892 Cov.: 30
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GnomAD3 exomes AF: 0.127 AC: 16826AN: 132704Hom.: 2742 AF XY: 0.105 AC XY: 7540AN XY: 71502
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GnomAD4 exome AF: 0.0612 AC: 76088AN: 1244104Hom.: 7292 Cov.: 25 AF XY: 0.0592 AC XY: 35820AN XY: 605190
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GnomAD4 genome AF: 0.207 AC: 31339AN: 151544Hom.: 6922 Cov.: 30 AF XY: 0.206 AC XY: 15269AN XY: 74010
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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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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at