chr1-113837817-T-C
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_015967.8(PTPN22):āc.1583A>Gā(p.Tyr528Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000137 in 1,613,782 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Consequence
NM_015967.8 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
PTPN22 | NM_015967.8 | c.1583A>G | p.Tyr528Cys | missense_variant | Exon 13 of 21 | NP_057051.4 | ||
PTPN22 | NM_001308297.2 | c.1511A>G | p.Tyr504Cys | missense_variant | Exon 12 of 20 | NP_001295226.2 | ||
PTPN22 | NM_001193431.3 | c.1583A>G | p.Tyr528Cys | missense_variant | Exon 13 of 21 | NP_001180360.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
PTPN22 | ENST00000359785.10 | c.1583A>G | p.Tyr528Cys | missense_variant | Exon 13 of 21 | 1 | ENSP00000352833.5 |
Frequencies
GnomAD3 genomes AF: 0.000118 AC: 18AN: 152172Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000135 AC: 34AN: 251418Hom.: 0 AF XY: 0.000147 AC XY: 20AN XY: 135880
GnomAD4 exome AF: 0.000139 AC: 203AN: 1461610Hom.: 0 Cov.: 31 AF XY: 0.000124 AC XY: 90AN XY: 727126
GnomAD4 genome AF: 0.000118 AC: 18AN: 152172Hom.: 0 Cov.: 32 AF XY: 0.0000673 AC XY: 5AN XY: 74336
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.1583A>G (p.Y528C) alteration is located in exon 13 (coding exon 13) of the PTPN22 gene. This alteration results from a A to G substitution at nucleotide position 1583, causing the tyrosine (Y) at amino acid position 528 to be replaced by a cysteine (C). 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