chr11-18740694-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_006906.2(PTPN5):c.824G>A(p.Arg275His) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000185 in 1,609,086 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_006906.2 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 |
---|---|---|---|---|---|---|---|
PTPN5 | NM_006906.2 | c.824G>A | p.Arg275His | missense_variant | 8/15 | ENST00000358540.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PTPN5 | ENST00000358540.7 | c.824G>A | p.Arg275His | missense_variant | 8/15 | 1 | NM_006906.2 | ||
PTPN5 | ENST00000396168.1 | c.752G>A | p.Arg251His | missense_variant | 7/14 | 1 | P1 | ||
PTPN5 | ENST00000396170.5 | c.728G>A | p.Arg243His | missense_variant | 8/15 | 2 | |||
PTPN5 | ENST00000477854.5 | c.236G>A | p.Arg79His | missense_variant | 4/11 | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.000151 AC: 23AN: 151888Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000145 AC: 36AN: 248038Hom.: 0 AF XY: 0.000127 AC XY: 17AN XY: 134104
GnomAD4 exome AF: 0.000189 AC: 275AN: 1457198Hom.: 0 Cov.: 30 AF XY: 0.000182 AC XY: 132AN XY: 724586
GnomAD4 genome ? AF: 0.000151 AC: 23AN: 151888Hom.: 0 Cov.: 32 AF XY: 0.000162 AC XY: 12AN XY: 74154
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Oct 12, 2021 | The c.824G>A (p.R275H) alteration is located in exon 8 (coding exon 7) of the PTPN5 gene. This alteration results from a G to A substitution at nucleotide position 824, causing the arginine (R) at amino acid position 275 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