8-144429144-C-T
Variant names:
Variant summary
Our verdict is Likely benign. The variant received -3 ACMG points: 2P and 5B. PM2BP4_ModerateBP6_ModerateBP7
The NM_013432.5(TONSL):c.4136G>A(p.Ter1379Ter) variant causes a stop retained change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000145 in 1,375,830 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
TONSL
NM_013432.5 stop_retained
NM_013432.5 stop_retained
Scores
2
Clinical Significance
Conservation
PhyloP100: 1.29
Genes affected
TONSL (HGNC:7801): (tonsoku like, DNA repair protein) The protein encoded by this gene is thought to be a negative regulator of NF-kappa-B mediated transcription. The encoded protein may bind NF-kappa-B complexes and trap them in the cytoplasm, preventing them from entering the nucleus and interacting with the DNA. Phosphorylation of this protein targets it for degradation by the ubiquitination pathway, which frees the NF-kappa-B complexes to enter the nucleus. [provided by RefSeq, Jul 2008]
Genome browser will be placed here
ACMG classification
Classification was made for transcript
Our verdict: Likely_benign. The variant received -3 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.34).
BP6
Variant 8-144429144-C-T is Benign according to our data. Variant chr8-144429144-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 2803119.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
Synonymous conserved (PhyloP=1.29 with no splicing effect.
Transcripts
RefSeq
| Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|
| TONSL | NM_013432.5 | c.4136G>A | p.Ter1379Ter | stop_retained_variant | Exon 26 of 26 | ENST00000409379.8 | NP_038460.4 | |
| TONSL | XM_011517048.3 | c.3164G>A | p.Ter1055Ter | stop_retained_variant | Exon 19 of 19 | XP_011515350.1 | ||
| TONSL | XM_011517049.3 | c.3128G>A | p.Ter1043Ter | stop_retained_variant | Exon 19 of 19 | XP_011515351.1 |
Ensembl
| Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
|---|---|---|---|---|---|---|---|---|---|---|
| TONSL | ENST00000409379.8 | c.4136G>A | p.Ter1379Ter | stop_retained_variant | Exon 26 of 26 | 1 | NM_013432.5 | ENSP00000386239.3 | ||
| TONSL | ENST00000497613.2 | n.6238G>A | non_coding_transcript_exon_variant | Exon 17 of 17 | 2 | |||||
| ENSG00000305609 | ENST00000811933.1 | n.199+1030C>T | intron_variant | Intron 1 of 1 |
Frequencies
GnomAD3 genomes
GnomAD3 genomes
Cov.:
33
GnomAD4 exome AF: 0.00000145 AC: 2AN: 1375830Hom.: 0 Cov.: 31 AF XY: 0.00000295 AC XY: 2AN XY: 678620 show subpopulations
GnomAD4 exome
AF:
AC:
2
AN:
1375830
Hom.:
Cov.:
31
AF XY:
AC XY:
2
AN XY:
678620
show subpopulations
African (AFR)
AF:
AC:
1
AN:
30524
American (AMR)
AF:
AC:
0
AN:
34460
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
24944
East Asian (EAS)
AF:
AC:
0
AN:
35138
South Asian (SAS)
AF:
AC:
0
AN:
78604
European-Finnish (FIN)
AF:
AC:
0
AN:
35292
Middle Eastern (MID)
AF:
AC:
0
AN:
4406
European-Non Finnish (NFE)
AF:
AC:
1
AN:
1075014
Other (OTH)
AF:
AC:
0
AN:
57448
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
Alfa
AF:
Hom.:
ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Apr 09, 2023
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
RBP_binding_hub_radar
RBP_regulation_power_radar
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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