chr12-70746080-A-G
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2
The NM_002849.4(PTPRR):c.745T>C(p.Tyr249His) variant causes a missense change. The variant allele was found at a frequency of 0.00137 in 1,610,622 control chromosomes in the GnomAD database, including 45 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★). Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.
Frequency
Consequence
NM_002849.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -10 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PTPRR | NM_002849.4 | c.745T>C | p.Tyr249His | missense_variant | 6/14 | ENST00000283228.7 | |
LOC124902960 | XR_007063361.1 | n.628+26257A>G | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PTPRR | ENST00000283228.7 | c.745T>C | p.Tyr249His | missense_variant | 6/14 | 1 | NM_002849.4 | P3 |
Frequencies
GnomAD3 genomes ? AF: 0.00131 AC: 200AN: 152160Hom.: 2 Cov.: 32
GnomAD3 exomes AF: 0.00257 AC: 636AN: 247304Hom.: 13 AF XY: 0.00253 AC XY: 339AN XY: 133778
GnomAD4 exome AF: 0.00138 AC: 2012AN: 1458462Hom.: 43 Cov.: 33 AF XY: 0.00143 AC XY: 1037AN XY: 725614
GnomAD4 genome ? AF: 0.00131 AC: 200AN: 152160Hom.: 2 Cov.: 32 AF XY: 0.00125 AC XY: 93AN XY: 74332
ClinVar
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Aug 01, 2022 | PTPRR: BS2 - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at