rs150748717
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 2P and 10B. PM2BP4_StrongBP6_ModerateBS1
The NM_001330588.2(TPP2):c.3580-8C>T variant causes a splice region, splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000774 in 1,584,876 control chromosomes in the GnomAD database, including 1 homozygotes. 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, splice_polypyrimidine_tract, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -8 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TPP2 | NM_001330588.2 | c.3580-8C>T | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | ENST00000376052.5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TPP2 | ENST00000376052.5 | c.3580-8C>T | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | 5 | NM_001330588.2 | A1 |
Frequencies
GnomAD3 genomes AF: 0.000716 AC: 109AN: 152140Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000663 AC: 156AN: 235146Hom.: 1 AF XY: 0.000660 AC XY: 84AN XY: 127204
GnomAD4 exome AF: 0.000780 AC: 1117AN: 1432618Hom.: 1 Cov.: 30 AF XY: 0.000738 AC XY: 526AN XY: 712700
GnomAD4 genome AF: 0.000716 AC: 109AN: 152258Hom.: 0 Cov.: 33 AF XY: 0.000645 AC XY: 48AN XY: 74430
ClinVar
Submissions by phenotype
Evans syndrome, immunodeficiency, and premature immunosenescence associated with tripeptidyl-peptidase II deficiency Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jan 31, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at