rs587777987
Variant names:
Your query was ambiguous. Multiple possible variants found:
Variant summary
Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2BP4_Strong
The ENST00000475523.5(TNFRSF14):n.145T>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000242 in 1,237,118 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: not found (cov: 33)
Exomes 𝑓: 0.0000024 ( 0 hom. )
Consequence
TNFRSF14
ENST00000475523.5 non_coding_transcript_exon
ENST00000475523.5 non_coding_transcript_exon
Scores
2
Clinical Significance
Conservation
PhyloP100: -1.37
Publications
0 publications found
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]
Genome browser will be placed here
ACMG classification
Classification was made for transcript
Our verdict: Likely_benign. The variant received -2 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.84).
Variant Effect in Transcripts
ACMG analysis was done for transcript: ENST00000475523.5. You can select a different transcript below to see updated ACMG assignments.
RefSeq Transcripts
| Selected | Gene | Transcript | Tags | HGVSc | HGVSp | Effect | Exon Rank | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|---|
| TNFRSF14 | NM_003820.4 | MANE Select | c.305-397T>A | intron | N/A | NP_003811.2 | |||
| TNFRSF14 | NM_001297605.2 | c.305-397T>A | intron | N/A | NP_001284534.1 |
Ensembl Transcripts
| Selected | Gene | Transcript | Tags | HGVSc | HGVSp | Effect | Exon Rank | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|---|
| TNFRSF14 | ENST00000475523.5 | TSL:1 | n.145T>A | non_coding_transcript_exon | Exon 2 of 6 | ||||
| TNFRSF14 | ENST00000355716.5 | TSL:1 MANE Select | c.305-397T>A | intron | N/A | ENSP00000347948.4 | |||
| TNFRSF14 | ENST00000463471.6 | TSL:2 | n.1356T>A | non_coding_transcript_exon | Exon 3 of 5 |
Frequencies
GnomAD3 genomes
GnomAD3 genomes
Cov.:
33
GnomAD4 exome AF: 0.00000242 AC: 3AN: 1237118Hom.: 0 Cov.: 30 AF XY: 0.00000331 AC XY: 2AN XY: 605012 show subpopulations ⚠️ The allele balance in gnomAD version 4 Exomes is significantly skewed from the expected value of 0.5.
GnomAD4 exome
AF:
AC:
3
AN:
1237118
Hom.:
Cov.:
30
AF XY:
AC XY:
2
AN XY:
605012
show subpopulations
⚠️ The allele balance in gnomAD version 4 Exomes is significantly skewed from the expected value of 0.5.
African (AFR)
AF:
AC:
0
AN:
28726
American (AMR)
AF:
AC:
0
AN:
31172
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
21548
East Asian (EAS)
AF:
AC:
0
AN:
24470
South Asian (SAS)
AF:
AC:
0
AN:
77072
European-Finnish (FIN)
AF:
AC:
0
AN:
15194
Middle Eastern (MID)
AF:
AC:
0
AN:
4994
European-Non Finnish (NFE)
AF:
AC:
3
AN:
984586
Other (OTH)
AF:
AC:
0
AN:
49356
⚠️ The allele balance in gnomAD4 Exomes is highly skewed from 0.5 (p-value = 0.00131091), which strongly suggests a high chance of mosaicism in these individuals.
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.392
Heterozygous variant carriers
0
0
1
1
2
2
0.00
0.20
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0.60
0.80
0.95
Allele balance
Age Distribution
Exome Het
Variant carriers
0
2
4
6
8
10
<30
30-35
35-40
40-45
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>80
Age
GnomAD4 genome
GnomAD4 genome
Cov.:
33
Alfa
AF:
Hom.:
ClinVar
Significance: not provided
Submissions summary: Other:1
Revision: no classification provided
LINK: link
Submissions by phenotype
not specified Other:1
Sep 19, 2013
ITMI
Significance:not provided
Review Status:no classification provided
Collection Method:reference population
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
DANN
Benign
PhyloP100
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
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