chr12-70761538-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_002849.4(PTPRR):c.560G>A(p.Arg187His) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000813 in 1,612,248 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_002849.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PTPRR | NM_002849.4 | c.560G>A | p.Arg187His | missense_variant | 4/14 | ENST00000283228.7 | |
LOC124902960 | XR_007063361.1 | n.629-11899C>T | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PTPRR | ENST00000283228.7 | c.560G>A | p.Arg187His | missense_variant | 4/14 | 1 | NM_002849.4 | P3 | |
PTPRR | ENST00000342084.8 | c.224G>A | p.Arg75His | missense_variant | 3/13 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.000105 AC: 16AN: 152118Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000116 AC: 29AN: 250720Hom.: 0 AF XY: 0.000111 AC XY: 15AN XY: 135584
GnomAD4 exome AF: 0.0000788 AC: 115AN: 1460130Hom.: 0 Cov.: 30 AF XY: 0.0000840 AC XY: 61AN XY: 726462
GnomAD4 genome ? AF: 0.000105 AC: 16AN: 152118Hom.: 0 Cov.: 32 AF XY: 0.0000807 AC XY: 6AN XY: 74312
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jun 07, 2022 | The c.560G>A (p.R187H) alteration is located in exon 4 (coding exon 4) of the PTPRR gene. This alteration results from a G to A substitution at nucleotide position 560, causing the arginine (R) at amino acid position 187 to be replaced by a histidine (H). 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