rs565961218
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Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_003820.4(TNFRSF14):c.305-654A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000827 in 1,367,034 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 not provided (no stars).
Frequency
Genomes: 𝑓 0.00026 ( 0 hom., cov: 33)
Exomes 𝑓: 0.000060 ( 0 hom. )
Consequence
TNFRSF14
NM_003820.4 intron
NM_003820.4 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.971
Genes affected
TNFRSF14 (HGNC:11912): (TNF receptor superfamily member 14) This gene encodes a member of the TNF (tumor necrosis factor) receptor superfamily. The encoded protein functions in signal transduction pathways that activate inflammatory and inhibitory T-cell immune response. It binds herpes simplex virus (HSV) viral envelope glycoprotein D (gD), mediating its entry into cells. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jul 2014]
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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=-0.91).
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TNFRSF14 | NM_003820.4 | c.305-654A>G | intron_variant | ENST00000355716.5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TNFRSF14 | ENST00000355716.5 | c.305-654A>G | intron_variant | 1 | NM_003820.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.000263 AC: 40AN: 152238Hom.: 0 Cov.: 33
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GnomAD3 exomes AF: 0.000227 AC: 30AN: 132084Hom.: 0 AF XY: 0.000181 AC XY: 13AN XY: 71918
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GnomAD4 exome AF: 0.0000601 AC: 73AN: 1214678Hom.: 0 Cov.: 30 AF XY: 0.0000658 AC XY: 39AN XY: 592718
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GnomAD4 genome ? AF: 0.000263 AC: 40AN: 152356Hom.: 0 Cov.: 33 AF XY: 0.000322 AC XY: 24AN XY: 74506
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ClinVar
Significance: not provided
Submissions summary: Other:1
Revision: no classification provided
LINK: link
Submissions by phenotype
not specified Other:1
not provided, no classification provided | reference population | ITMI | Sep 19, 2013 | - - |
Computational scores
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Name
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
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