1-113837773-T-C
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP6_Very_StrongBS2
The NM_015967.8(PTPN22):āc.1627A>Gā(p.Ser543Gly) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000448 in 1,613,910 control chromosomes in the GnomAD database, including 6 homozygotes. In-silico tool predicts a benign outcome for this variant. 12/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (ā ā ).
Frequency
Consequence
NM_015967.8 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Benign. Variant got -12 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
PTPN22 | NM_015967.8 | c.1627A>G | p.Ser543Gly | missense_variant | Exon 13 of 21 | NP_057051.4 | ||
PTPN22 | NM_001308297.2 | c.1555A>G | p.Ser519Gly | missense_variant | Exon 12 of 20 | NP_001295226.2 | ||
PTPN22 | NM_001193431.3 | c.1627A>G | p.Ser543Gly | 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.1627A>G | p.Ser543Gly | missense_variant | Exon 13 of 21 | 1 | ENSP00000352833.5 |
Frequencies
GnomAD3 genomes AF: 0.00226 AC: 344AN: 152160Hom.: 4 Cov.: 32
GnomAD3 exomes AF: 0.000621 AC: 156AN: 251394Hom.: 1 AF XY: 0.000449 AC XY: 61AN XY: 135870
GnomAD4 exome AF: 0.000258 AC: 377AN: 1461632Hom.: 2 Cov.: 31 AF XY: 0.000239 AC XY: 174AN XY: 727138
GnomAD4 genome AF: 0.00227 AC: 346AN: 152278Hom.: 4 Cov.: 32 AF XY: 0.00220 AC XY: 164AN XY: 74462
ClinVar
Submissions by phenotype
not provided Benign:2
- -
- -
PTPN22-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