1-1211591-C-T
Variant names:
Variant summary
Our verdict is Likely benign. The variant received -5 ACMG points: 2P and 7B. PM2BP4_StrongBP6_ModerateBP7
The NM_003327.4(TNFRSF4):c.798G>A(p.Glu266Glu) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000146 in 1,372,744 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: not found (cov: 33)
Exomes 𝑓: 0.0000015 ( 0 hom. )
Consequence
TNFRSF4
NM_003327.4 synonymous
NM_003327.4 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.292
Publications
0 publications found
Genes affected
TNFRSF4 (HGNC:11918): (TNF receptor superfamily member 4) The protein encoded by this gene is a member of the TNF-receptor superfamily. This receptor has been shown to activate NF-kappaB through its interaction with adaptor proteins TRAF2 and TRAF5. Knockout studies in mice suggested that this receptor promotes the expression of apoptosis inhibitors BCL2 and BCL2lL1/BCL2-XL, and thus suppresses apoptosis. The knockout studies also suggested the roles of this receptor in CD4+ T cell response, as well as in T cell-dependent B cell proliferation and differentiation. [provided by RefSeq, Jul 2008]
TNFRSF4 Gene-Disease associations (from GenCC):
- combined immunodeficiency due to OX40 deficiencyInheritance: AR, Unknown Classification: SUPPORTIVE, LIMITED Submitted by: Ambry Genetics, ClinGen, Orphanet, Labcorp Genetics (formerly Invitae)
Genome browser will be placed here
ACMG classification
Classification was made for transcript
Our verdict: Likely_benign. The variant received -5 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.47).
BP6
Variant 1-1211591-C-T is Benign according to our data. Variant chr1-1211591-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 1155856.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
Synonymous conserved (PhyloP=-0.292 with no splicing effect.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes
GnomAD3 genomes
Cov.:
33
GnomAD4 exome AF: 0.00000146 AC: 2AN: 1372744Hom.: 0 Cov.: 30 AF XY: 0.00000148 AC XY: 1AN XY: 675174 show subpopulations
GnomAD4 exome
AF:
AC:
2
AN:
1372744
Hom.:
Cov.:
30
AF XY:
AC XY:
1
AN XY:
675174
show subpopulations
African (AFR)
AF:
AC:
2
AN:
29442
American (AMR)
AF:
AC:
0
AN:
30242
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
20766
East Asian (EAS)
AF:
AC:
0
AN:
36910
South Asian (SAS)
AF:
AC:
0
AN:
73524
European-Finnish (FIN)
AF:
AC:
0
AN:
50262
Middle Eastern (MID)
AF:
AC:
0
AN:
5370
European-Non Finnish (NFE)
AF:
AC:
0
AN:
1069862
Other (OTH)
AF:
AC:
0
AN:
56366
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.475
Heterozygous variant carriers
0
0
1
1
2
2
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
GnomAD4 genome
GnomAD4 genome
Cov.:
33
ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
Combined immunodeficiency due to OX40 deficiency Benign:1
Oct 26, 2020
Labcorp Genetics (formerly Invitae), Labcorp
Significance:Likely benign
Review Status:criteria provided, single submitter
Collection Method:clinical testing
- -
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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