1-29259881-G-A
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6BP7BS2
The NM_133178.4(PTPRU):c.687G>A(p.Gly229Gly) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000308 in 1,531,056 control chromosomes in the GnomAD database, including 3 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (no stars).
Frequency
Consequence
NM_133178.4 synonymous
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 rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
PTPRU | NM_133178.4 | c.687G>A | p.Gly229Gly | synonymous_variant | Exon 6 of 30 | ENST00000373779.8 | NP_573439.2 | |
PTPRU | NM_005704.5 | c.687G>A | p.Gly229Gly | synonymous_variant | Exon 6 of 31 | NP_005695.3 | ||
PTPRU | NM_133177.4 | c.687G>A | p.Gly229Gly | synonymous_variant | Exon 6 of 31 | NP_573438.3 | ||
PTPRU | NM_001195001.2 | c.687G>A | p.Gly229Gly | synonymous_variant | Exon 6 of 30 | NP_001181930.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
PTPRU | ENST00000373779.8 | c.687G>A | p.Gly229Gly | synonymous_variant | Exon 6 of 30 | 1 | NM_133178.4 | ENSP00000362884.3 | ||
PTPRU | ENST00000345512.7 | c.687G>A | p.Gly229Gly | synonymous_variant | Exon 6 of 31 | 1 | ENSP00000334941.5 | |||
PTPRU | ENST00000460170.2 | c.687G>A | p.Gly229Gly | synonymous_variant | Exon 6 of 31 | 1 | ENSP00000432906.1 | |||
PTPRU | ENST00000428026.6 | c.687G>A | p.Gly229Gly | synonymous_variant | Exon 6 of 30 | 1 | ENSP00000392332.2 |
Frequencies
GnomAD3 genomes AF: 0.000407 AC: 62AN: 152192Hom.: 1 Cov.: 32
GnomAD3 exomes AF: 0.00118 AC: 150AN: 127500Hom.: 0 AF XY: 0.00115 AC XY: 80AN XY: 69742
GnomAD4 exome AF: 0.000297 AC: 409AN: 1378750Hom.: 2 Cov.: 33 AF XY: 0.000313 AC XY: 213AN XY: 680012
GnomAD4 genome AF: 0.000414 AC: 63AN: 152306Hom.: 1 Cov.: 32 AF XY: 0.000510 AC XY: 38AN XY: 74470
ClinVar
Submissions by phenotype
PTPRU-related disorder Benign:1
This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at