rs73578896
Variant summary
Our verdict is Benign. Variant got -19 ACMG points: 1P and 20B. PP2BP4_StrongBP6_Very_StrongBS1BS2
The NM_001330588.2(TPP2):c.1534G>A(p.Val512Ile) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000577 in 1,612,336 control chromosomes in the GnomAD database, including 10 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Consequence
NM_001330588.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -19 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
TPP2 | NM_001330588.2 | c.1534G>A | p.Val512Ile | missense_variant | 13/30 | ENST00000376052.5 | NP_001317517.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
TPP2 | ENST00000376052.5 | c.1534G>A | p.Val512Ile | missense_variant | 13/30 | 5 | NM_001330588.2 | ENSP00000365220.3 |
Frequencies
GnomAD3 genomes AF: 0.00313 AC: 476AN: 151852Hom.: 4 Cov.: 32
GnomAD3 exomes AF: 0.000740 AC: 185AN: 250024Hom.: 1 AF XY: 0.000547 AC XY: 74AN XY: 135214
GnomAD4 exome AF: 0.000310 AC: 452AN: 1460366Hom.: 6 Cov.: 30 AF XY: 0.000266 AC XY: 193AN XY: 726498
GnomAD4 genome AF: 0.00315 AC: 479AN: 151970Hom.: 4 Cov.: 32 AF XY: 0.00310 AC XY: 230AN XY: 74282
ClinVar
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | not provided | Breakthrough Genomics, Breakthrough Genomics | - | - - |
Evans syndrome, immunodeficiency, and premature immunosenescence associated with tripeptidyl-peptidase II deficiency Benign:1
Benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Dec 02, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at