rs1217389
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The ENST00000359785.10(PTPN22):c.2281+2012G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.761 in 151,866 control chromosomes in the GnomAD database, including 44,692 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.76 ( 44689 hom., cov: 32)
Exomes 𝑓: 0.64 ( 3 hom. )
Consequence
PTPN22
ENST00000359785.10 intron
ENST00000359785.10 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.389
Genes affected
PTPN22 (HGNC:9652): (protein tyrosine phosphatase non-receptor type 22) This gene encodes of member of the non-receptor class 4 subfamily of the protein-tyrosine phosphatase family. The encoded protein is a lymphoid-specific intracellular phosphatase that associates with the molecular adapter protein CBL and may be involved in regulating CBL function in the T-cell receptor signaling pathway. Mutations in this gene may be associated with a range of autoimmune disorders including Type 1 Diabetes, rheumatoid arthritis, systemic lupus erythematosus and Graves' disease. Alternatively spliced transcript variants encoding distinct isoforms have been described. [provided by RefSeq, Mar 2009]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.95).
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.871 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PTPN22 | NM_015967.8 | c.2281+2012G>A | intron_variant | ENST00000359785.10 | |||
PTPN22 | XM_047417630.1 | c.2131+2012G>A | intron_variant | ||||
AP4B1-AS1 | NR_125965.1 | n.414+7658C>T | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PTPN22 | ENST00000359785.10 | c.2281+2012G>A | intron_variant | 1 | NM_015967.8 | P1 | |||
ENST00000664434.1 | n.418+7658C>T | intron_variant, non_coding_transcript_variant |
Frequencies
GnomAD3 genomes ? AF: 0.761 AC: 115466AN: 151734Hom.: 44641 Cov.: 32
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GnomAD4 exome AF: 0.643 AC: 9AN: 14Hom.: 3 Cov.: 0 AF XY: 0.667 AC XY: 8AN XY: 12
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GnomAD4 genome ? AF: 0.761 AC: 115575AN: 151852Hom.: 44689 Cov.: 32 AF XY: 0.754 AC XY: 55999AN XY: 74224
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ClinVar
Not reported inComputational scores
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Calibrated prediction
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at