1-113830026-A-G
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_015967.8(PTPN22):āc.2057T>Cā(p.Leu686Pro) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000139 in 1,439,782 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/19 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/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
PTPN22 | NM_015967.8 | c.2057T>C | p.Leu686Pro | missense_variant | 17/21 | NP_057051.4 | ||
PTPN22 | NM_001308297.1 | c.1985T>C | p.Leu662Pro | missense_variant | 16/20 | NP_001295226.2 | ||
PTPN22 | NM_001193431.2 | c.1973T>C | p.Leu658Pro | missense_variant | 17/21 | NP_001180360.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
PTPN22 | ENST00000359785.10 | c.2057T>C | p.Leu686Pro | missense_variant | 17/21 | 1 | ENSP00000352833.5 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 exomes AF: 0.00000807 AC: 2AN: 247730Hom.: 0 AF XY: 0.00000746 AC XY: 1AN XY: 134000
GnomAD4 exome AF: 0.00000139 AC: 2AN: 1439782Hom.: 0 Cov.: 30 AF XY: 0.00000279 AC XY: 2AN XY: 717414
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jun 17, 2024 | The c.2057T>C (p.L686P) alteration is located in exon 17 (coding exon 17) of the PTPN22 gene. This alteration results from a T to C substitution at nucleotide position 2057, causing the leucine (L) at amino acid position 686 to be replaced by a proline (P). 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