1-7933147-T-C
Variant names:
Variant summary
Our verdict is Likely benign. The variant received -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6_Moderate
The NM_001561.6(TNFRSF9):c.679+15A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: not found (cov: 32)
Exomes 𝑓: 0.0 ( 0 hom. )
Failed GnomAD Quality Control
Consequence
TNFRSF9
NM_001561.6 intron
NM_001561.6 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.341
Publications
0 publications found
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]
TNFRSF9 Gene-Disease associations (from GenCC):
- immunodeficiency 109 with lymphoproliferationInheritance: AR Classification: DEFINITIVE, STRONG, MODERATE Submitted by: PanelApp Australia, ClinGen, Labcorp Genetics (formerly Invitae), Ambry Genetics
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ACMG classification
Classification was made for transcript
Our verdict: Likely_benign. The variant received -4 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.86).
BP6
Variant 1-7933147-T-C is Benign according to our data. Variant chr1-7933147-T-C is described in ClinVar as Likely_benign. ClinVar VariationId is 3615076.Status of the report is criteria_provided_single_submitter, 1 stars.
Variant Effect in Transcripts
ACMG analysis was done for transcript: NM_001561.6. You can select a different transcript below to see updated ACMG assignments.
Ensembl Transcripts
Frequencies
GnomAD3 genomes
GnomAD3 genomes
Cov.:
32
GnomAD2 exomes AF: 0.00 AC: 0AN: 236940 AF XY: 0.00
GnomAD2 exomes
AF:
AC:
0
AN:
236940
AF XY:
Gnomad AFR exome
AF:
Gnomad AMR exome
AF:
Gnomad ASJ exome
AF:
Gnomad EAS exome
AF:
Gnomad FIN exome
AF:
Gnomad NFE exome
AF:
Gnomad OTH exome
AF:
GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0AN: 1441236Hom.: 0 Cov.: 30 AF XY: 0.00 AC XY: 0AN XY: 715234
GnomAD4 exome
Data not reliable, filtered out with message: AC0
AF:
AC:
0
AN:
1441236
Hom.:
Cov.:
30
AF XY:
AC XY:
0
AN XY:
715234
African (AFR)
AF:
AC:
0
AN:
32406
American (AMR)
AF:
AC:
0
AN:
40242
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
25434
East Asian (EAS)
AF:
AC:
0
AN:
39310
South Asian (SAS)
AF:
AC:
0
AN:
82700
European-Finnish (FIN)
AF:
AC:
0
AN:
53224
Middle Eastern (MID)
AF:
AC:
0
AN:
5692
European-Non Finnish (NFE)
AF:
AC:
0
AN:
1102738
Other (OTH)
AF:
AC:
0
AN:
59490
GnomAD4 genome
GnomAD4 genome
Cov.:
32
ClinVar
ClinVar submissions
View on ClinVar Significance:Likely benign
Revision:criteria provided, single submitter
Pathogenic
VUS
Benign
Condition
-
-
1
not provided (1)
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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