chr19-5211696-G-A
Variant summary
Our verdict is Likely benign. Variant got -1 ACMG points: 3P and 4B. PP2PP3_ModerateBS2
The NM_002850.4(PTPRS):c.5128C>T(p.Arg1710Cys) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0000341 in 1,614,116 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R1710H) has been classified as Uncertain significance.
Frequency
Consequence
NM_002850.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PTPRS | NM_002850.4 | c.5128C>T | p.Arg1710Cys | missense_variant | 33/38 | ENST00000262963.11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PTPRS | ENST00000262963.11 | c.5128C>T | p.Arg1710Cys | missense_variant | 33/38 | 5 | NM_002850.4 | A1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000329 AC: 5AN: 152182Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000517 AC: 13AN: 251320Hom.: 0 AF XY: 0.0000515 AC XY: 7AN XY: 135910
GnomAD4 exome AF: 0.0000342 AC: 50AN: 1461816Hom.: 0 Cov.: 33 AF XY: 0.0000316 AC XY: 23AN XY: 727196
GnomAD4 genome ? AF: 0.0000328 AC: 5AN: 152300Hom.: 0 Cov.: 33 AF XY: 0.0000134 AC XY: 1AN XY: 74472
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jan 16, 2024 | The c.5128C>T (p.R1710C) alteration is located in exon 33 (coding exon 32) of the PTPRS gene. This alteration results from a C to T substitution at nucleotide position 5128, causing the arginine (R) at amino acid position 1710 to be replaced by a cysteine (C). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at