chr11-18481759-G-A
Variant names:
Variant summary
Our verdict is Benign. The variant received -19 ACMG points: 0P and 19B. BP4_ModerateBP6_Very_StrongBP7BA1
The NM_006292.4(TSG101):c.954C>T(p.Ile318Ile) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00474 in 1,614,136 control chromosomes in the GnomAD database, including 281 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Genomes: 𝑓 0.024 ( 145 hom., cov: 32)
Exomes 𝑓: 0.0028 ( 136 hom. )
Consequence
TSG101
NM_006292.4 synonymous
NM_006292.4 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 2.01
Genes affected
TSG101 (HGNC:15971): (tumor susceptibility 101) The protein encoded by this gene belongs to a group of apparently inactive homologs of ubiquitin-conjugating enzymes. The gene product contains a coiled-coil domain that interacts with stathmin, a cytosolic phosphoprotein implicated in tumorigenesis. The protein may play a role in cell growth and differentiation and act as a negative growth regulator. In vitro steady-state expression of this tumor susceptibility gene appears to be important for maintenance of genomic stability and cell cycle regulation. Mutations and alternative splicing in this gene occur in high frequency in breast cancer and suggest that defects occur during breast cancer tumorigenesis and/or progression. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification was made for transcript
Our verdict: Benign. The variant received -19 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.32).
BP6
Variant 11-18481759-G-A is Benign according to our data. Variant chr11-18481759-G-A is described in ClinVar as [Benign]. Clinvar id is 774621.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BP7
Synonymous conserved (PhyloP=2.01 with no splicing effect.
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0792 is higher than 0.05.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0238 AC: 3626AN: 152168Hom.: 145 Cov.: 32 show subpopulations
GnomAD3 genomes
AF:
AC:
3626
AN:
152168
Hom.:
Cov.:
32
Gnomad AFR
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GnomAD2 exomes AF: 0.00626 AC: 1573AN: 251394 AF XY: 0.00449 show subpopulations
GnomAD2 exomes
AF:
AC:
1573
AN:
251394
AF XY:
Gnomad AFR exome
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GnomAD4 exome AF: 0.00275 AC: 4023AN: 1461850Hom.: 136 Cov.: 32 AF XY: 0.00243 AC XY: 1764AN XY: 727226 show subpopulations
GnomAD4 exome
AF:
AC:
4023
AN:
1461850
Hom.:
Cov.:
32
AF XY:
AC XY:
1764
AN XY:
727226
Gnomad4 AFR exome
AF:
AC:
2839
AN:
33478
Gnomad4 AMR exome
AF:
AC:
251
AN:
44724
Gnomad4 ASJ exome
AF:
AC:
0
AN:
26134
Gnomad4 EAS exome
AF:
AC:
0
AN:
39686
Gnomad4 SAS exome
AF:
AC:
15
AN:
86250
Gnomad4 FIN exome
AF:
AC:
2
AN:
53414
Gnomad4 NFE exome
AF:
AC:
503
AN:
1112002
Gnomad4 Remaining exome
AF:
AC:
366
AN:
60394
Heterozygous variant carriers
0
226
452
677
903
1129
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Exome Het
Exome Hom
Variant carriers
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Age
GnomAD4 genome AF: 0.0238 AC: 3630AN: 152286Hom.: 145 Cov.: 32 AF XY: 0.0230 AC XY: 1710AN XY: 74482 show subpopulations
GnomAD4 genome
AF:
AC:
3630
AN:
152286
Hom.:
Cov.:
32
AF XY:
AC XY:
1710
AN XY:
74482
Gnomad4 AFR
AF:
AC:
0.0814916
AN:
0.0814916
Gnomad4 AMR
AF:
AC:
0.00934518
AN:
0.00934518
Gnomad4 ASJ
AF:
AC:
0
AN:
0
Gnomad4 EAS
AF:
AC:
0
AN:
0
Gnomad4 SAS
AF:
AC:
0.00041425
AN:
0.00041425
Gnomad4 FIN
AF:
AC:
0
AN:
0
Gnomad4 NFE
AF:
AC:
0.000852565
AN:
0.000852565
Gnomad4 OTH
AF:
AC:
0.0184834
AN:
0.0184834
Heterozygous variant carriers
0
161
322
484
645
806
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Genome Het
Genome Hom
Variant carriers
0
36
72
108
144
180
<30
30-35
35-40
40-45
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50-55
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65-70
70-75
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>80
Age
Alfa
AF:
Hom.:
Bravo
AF:
Asia WGS
AF:
AC:
18
AN:
3478
ClinVar
Significance: Benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not provided Benign:2
-
Breakthrough Genomics, Breakthrough Genomics
Significance:Benign
Review Status:criteria provided, single submitter
Collection Method:not provided
- -
Aug 16, 2018
Labcorp Genetics (formerly Invitae), Labcorp
Significance:Benign
Review Status:criteria provided, single submitter
Collection Method:clinical testing
- -
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
DANN
Benign
Mutation Taster
=90/10
polymorphism (auto)
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