chr1-113837886-G-C
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The ENST00000359785.10(PTPN22):c.1514C>G(p.Ser505Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00125 in 1,614,104 control chromosomes in the GnomAD database, including 50 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/18 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Consequence
ENST00000359785.10 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PTPN22 | NM_015967.8 | c.1514C>G | p.Ser505Cys | missense_variant | 13/21 | ENST00000359785.10 | |
PTPN22 | XM_047417630.1 | c.1364C>G | p.Ser455Cys | missense_variant | 11/19 | ||
AP4B1-AS1 | NR_125965.1 | n.414+22414G>C | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PTPN22 | ENST00000359785.10 | c.1514C>G | p.Ser505Cys | missense_variant | 13/21 | 1 | NM_015967.8 | P1 | |
ENST00000664434.1 | n.470+6073G>C | intron_variant, non_coding_transcript_variant |
Frequencies
GnomAD3 genomes ? AF: 0.000887 AC: 135AN: 152164Hom.: 5 Cov.: 32
GnomAD3 exomes AF: 0.00284 AC: 714AN: 251372Hom.: 17 AF XY: 0.00363 AC XY: 493AN XY: 135856
GnomAD4 exome AF: 0.00129 AC: 1889AN: 1461822Hom.: 46 Cov.: 32 AF XY: 0.00180 AC XY: 1312AN XY: 727208
GnomAD4 genome ? AF: 0.000873 AC: 133AN: 152282Hom.: 4 Cov.: 32 AF XY: 0.00132 AC XY: 98AN XY: 74450
ClinVar
Submissions by phenotype
PTPN22-related disorder Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Apr 05, 2019 | 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). - |
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Dec 31, 2019 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at