rs1130496
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_002847.5(PTPRN2):c.638G>A(p.Arg213His) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.405 in 1,612,628 control chromosomes in the GnomAD database, including 135,075 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.
Frequency
Consequence
NM_002847.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -12 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PTPRN2 | NM_002847.5 | c.638G>A | p.Arg213His | missense_variant | 6/23 | ENST00000389418.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PTPRN2 | ENST00000389418.9 | c.638G>A | p.Arg213His | missense_variant | 6/23 | 1 | NM_002847.5 | P2 | |
PTPRN2 | ENST00000389416.8 | c.587G>A | p.Arg196His | missense_variant | 5/22 | 1 | A2 | ||
PTPRN2 | ENST00000389413.7 | c.638G>A | p.Arg213His | missense_variant | 6/22 | 1 | |||
PTPRN2 | ENST00000409483.5 | c.524G>A | p.Arg175His | missense_variant | 5/22 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.353 AC: 53570AN: 151678Hom.: 10478 Cov.: 32
GnomAD3 exomes AF: 0.404 AC: 100071AN: 247926Hom.: 20912 AF XY: 0.402 AC XY: 54047AN XY: 134390
GnomAD4 exome AF: 0.410 AC: 599044AN: 1460834Hom.: 124585 Cov.: 65 AF XY: 0.409 AC XY: 297004AN XY: 726738
GnomAD4 genome ? AF: 0.353 AC: 53591AN: 151794Hom.: 10490 Cov.: 32 AF XY: 0.354 AC XY: 26254AN XY: 74172
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at