NM_001330588.2:c.30C>T
Variant names:
Variant summary
Our verdict is Benign. The variant received -9 ACMG points: 0P and 9B. BP4_ModerateBP6_ModerateBP7BS1
The NM_001330588.2(TPP2):c.30C>T(p.Phe10Phe) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000161 in 1,612,120 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: 𝑓 0.000072 ( 0 hom., cov: 33)
Exomes 𝑓: 0.000010 ( 0 hom. )
Consequence
TPP2
NM_001330588.2 synonymous
NM_001330588.2 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 1.96
Publications
0 publications found
Genes affected
TPP2 (HGNC:12016): (tripeptidyl peptidase 2) This gene encodes a mammalian peptidase that, at neutral pH, removes tripeptides from the N terminus of longer peptides. The protein has a specialized function that is essential for some MHC class I antigen presentation. The protein is a high molecular mass serine exopeptidase; the amino acid sequence surrounding the serine residue at the active site is similar to the peptidases of the subtilisin class rather than the trypsin class. [provided by RefSeq, Jul 2008]
TPP2 Gene-Disease associations (from GenCC):
- immunodeficiency 78 with autoimmunity and developmental delayInheritance: AR Classification: DEFINITIVE, STRONG, MODERATE Submitted by: G2P, Labcorp Genetics (formerly Invitae), Ambry Genetics
- autoimmune hemolytic anemia-autoimmune thrombocytopenia-primary immunodeficiency syndromeInheritance: AR Classification: SUPPORTIVE Submitted by: Orphanet
Genome browser will be placed here
ACMG classification
Classification was made for transcript
Our verdict: Benign. The variant received -9 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.19).
BP6
Variant 13-102597068-C-T is Benign according to our data. Variant chr13-102597068-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 1099505.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
Synonymous conserved (PhyloP=1.96 with no splicing effect.
BS1
Variant frequency is greater than expected in population afr. GnomAd4 allele frequency = 0.0000722 (11/152326) while in subpopulation AFR AF = 0.00024 (10/41592). AF 95% confidence interval is 0.00013. There are 0 homozygotes in GnomAd4. There are 5 alleles in the male GnomAd4 subpopulation. Median coverage is 33. This position passed quality control check.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000723 AC: 11AN: 152208Hom.: 0 Cov.: 33 show subpopulations
GnomAD3 genomes
AF:
AC:
11
AN:
152208
Hom.:
Cov.:
33
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
GnomAD2 exomes AF: 0.0000121 AC: 3AN: 247814 AF XY: 0.00000742 show subpopulations
GnomAD2 exomes
AF:
AC:
3
AN:
247814
AF XY:
Gnomad AFR exome
AF:
Gnomad AMR exome
AF:
Gnomad ASJ exome
AF:
Gnomad EAS exome
AF:
Gnomad FIN exome
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Gnomad NFE exome
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Gnomad OTH exome
AF:
GnomAD4 exome AF: 0.0000103 AC: 15AN: 1459794Hom.: 0 Cov.: 31 AF XY: 0.00000413 AC XY: 3AN XY: 726204 show subpopulations
GnomAD4 exome
AF:
AC:
15
AN:
1459794
Hom.:
Cov.:
31
AF XY:
AC XY:
3
AN XY:
726204
show subpopulations
African (AFR)
AF:
AC:
13
AN:
33344
American (AMR)
AF:
AC:
0
AN:
44700
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
26080
East Asian (EAS)
AF:
AC:
0
AN:
39648
South Asian (SAS)
AF:
AC:
0
AN:
86156
European-Finnish (FIN)
AF:
AC:
0
AN:
53296
Middle Eastern (MID)
AF:
AC:
0
AN:
4802
European-Non Finnish (NFE)
AF:
AC:
2
AN:
1111546
Other (OTH)
AF:
AC:
0
AN:
60222
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.502
Heterozygous variant carriers
0
1
2
4
5
6
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
GnomAD4 genome AF: 0.0000722 AC: 11AN: 152326Hom.: 0 Cov.: 33 AF XY: 0.0000671 AC XY: 5AN XY: 74482 show subpopulations
GnomAD4 genome
AF:
AC:
11
AN:
152326
Hom.:
Cov.:
33
AF XY:
AC XY:
5
AN XY:
74482
show subpopulations
African (AFR)
AF:
AC:
10
AN:
41592
American (AMR)
AF:
AC:
0
AN:
15310
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
3472
East Asian (EAS)
AF:
AC:
0
AN:
5162
South Asian (SAS)
AF:
AC:
0
AN:
4826
European-Finnish (FIN)
AF:
AC:
0
AN:
10620
Middle Eastern (MID)
AF:
AC:
0
AN:
292
European-Non Finnish (NFE)
AF:
AC:
0
AN:
68024
Other (OTH)
AF:
AC:
1
AN:
2116
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.507
Heterozygous variant carriers
0
1
2
2
3
4
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Alfa
AF:
Hom.:
Bravo
AF:
ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
Evans syndrome, immunodeficiency, and premature immunosenescence associated with tripeptidyl-peptidase II deficiency Benign:1
Jul 21, 2024
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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