1-29236635-C-A
Variant summary
Our verdict is Benign. Variant got -7 ACMG points: 0P and 7B. BP4_ModerateBP6BS2
The NM_133178.4(PTPRU):c.-10C>A variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000314 in 1,261,350 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (no stars).
Frequency
Consequence
NM_133178.4 5_prime_UTR
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -7 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
PTPRU | NM_133178.4 | c.-10C>A | 5_prime_UTR_variant | Exon 1 of 30 | ENST00000373779.8 | NP_573439.2 | ||
PTPRU | NM_005704.5 | c.-10C>A | 5_prime_UTR_variant | Exon 1 of 31 | NP_005695.3 | |||
PTPRU | NM_133177.4 | c.-10C>A | 5_prime_UTR_variant | Exon 1 of 31 | NP_573438.3 | |||
PTPRU | NM_001195001.2 | c.-10C>A | 5_prime_UTR_variant | Exon 1 of 30 | NP_001181930.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
PTPRU | ENST00000373779 | c.-10C>A | 5_prime_UTR_variant | Exon 1 of 30 | 1 | NM_133178.4 | ENSP00000362884.3 | |||
PTPRU | ENST00000345512 | c.-10C>A | 5_prime_UTR_variant | Exon 1 of 31 | 1 | ENSP00000334941.5 | ||||
PTPRU | ENST00000428026 | c.-10C>A | 5_prime_UTR_variant | Exon 1 of 30 | 1 | ENSP00000392332.2 | ||||
PTPRU | ENST00000460170.2 | c.-10C>A | upstream_gene_variant | 1 | ENSP00000432906.1 |
Frequencies
GnomAD3 genomes AF: 0.00119 AC: 181AN: 151810Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00149 AC: 25AN: 16744Hom.: 0 AF XY: 0.00151 AC XY: 16AN XY: 10606
GnomAD4 exome AF: 0.000194 AC: 215AN: 1109428Hom.: 0 Cov.: 30 AF XY: 0.000221 AC XY: 117AN XY: 530546
GnomAD4 genome AF: 0.00119 AC: 181AN: 151922Hom.: 0 Cov.: 32 AF XY: 0.00135 AC XY: 100AN XY: 74278
ClinVar
Submissions by phenotype
PTPRU-related disorder Benign:1
This variant is classified as likely 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