chr13-102674498-T-G
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 2P and 16B. PM2BP4_StrongBP6_Very_StrongBS1
The NM_001330588.2(TPP2):c.3579+8T>G variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00013 in 1,613,274 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Consequence
NM_001330588.2 splice_region, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -14 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TPP2 | NM_001330588.2 | c.3579+8T>G | splice_region_variant, intron_variant | ENST00000376052.5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TPP2 | ENST00000376052.5 | c.3579+8T>G | splice_region_variant, intron_variant | 5 | NM_001330588.2 | A1 |
Frequencies
GnomAD3 genomes AF: 0.000756 AC: 115AN: 152202Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000160 AC: 40AN: 250298Hom.: 0 AF XY: 0.000111 AC XY: 15AN XY: 135368
GnomAD4 exome AF: 0.0000650 AC: 95AN: 1460954Hom.: 0 Cov.: 31 AF XY: 0.0000633 AC XY: 46AN XY: 726770
GnomAD4 genome AF: 0.000755 AC: 115AN: 152320Hom.: 0 Cov.: 33 AF XY: 0.000779 AC XY: 58AN XY: 74482
ClinVar
Submissions by phenotype
TPP2-related disorder Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Apr 25, 2019 | This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Evans syndrome, immunodeficiency, and premature immunosenescence associated with tripeptidyl-peptidase II deficiency Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jan 25, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at