12-70761588-T-C
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_002849.4(PTPRR):āc.510A>Gā(p.Ile170Met) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000959 in 1,459,438 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Consequence
NM_002849.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PTPRR | NM_002849.4 | c.510A>G | p.Ile170Met | missense_variant | 4/14 | ENST00000283228.7 | |
LOC124902960 | XR_007063361.1 | n.629-11849T>C | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PTPRR | ENST00000283228.7 | c.510A>G | p.Ile170Met | missense_variant | 4/14 | 1 | NM_002849.4 | P3 | |
PTPRR | ENST00000342084.8 | c.174A>G | p.Ile58Met | missense_variant | 3/13 | 2 |
Frequencies
GnomAD3 genomes AF: 0.00 AC: 1AN: 152216Hom.: 0 Cov.: 32 FAILED QC
GnomAD4 exome AF: 0.00000959 AC: 14AN: 1459438Hom.: 0 Cov.: 30 AF XY: 0.00000964 AC XY: 7AN XY: 726146
GnomAD4 genome Data not reliable, filtered out with message: AS_VQSR AF: 0.00000657 AC: 1AN: 152216Hom.: 0 Cov.: 32 AF XY: 0.0000134 AC XY: 1AN XY: 74372
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Nov 14, 2023 | The c.510A>G (p.I170M) alteration is located in exon 4 (coding exon 4) of the PTPRR gene. This alteration results from a A to G substitution at nucleotide position 510, causing the isoleucine (I) at amino acid position 170 to be replaced by a methionine (M). 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