rs35281969
Variant names:
Your query was ambiguous. Multiple possible variants found:
Variant summary
Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_015967.8(PTPN22):c.829-34G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000126 in 1,423,768 control chromosomes in the GnomAD database, with no homozygous occurrence. 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 0.0 ( 0 hom., cov: 32)
Exomes 𝑓: 0.000013 ( 0 hom. )
Failed GnomAD Quality Control
Consequence
PTPN22
NM_015967.8 intron
NM_015967.8 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.321
Publications
0 publications found
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]
Genome browser will be placed here
ACMG classification
Classification was made for transcript
Our verdict: Likely_benign. The variant received -2 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.82).
Variant Effect in Transcripts
ACMG analysis was done for transcript: NM_015967.8. You can select a different transcript below to see updated ACMG assignments.
RefSeq Transcripts
| Sel. | Gene | Transcript | Tags | HGVSc | HGVSp | Effect | Exon Rank | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|---|
| PTPN22 | NM_015967.8 | MANE Select | c.829-34G>T | intron | N/A | NP_057051.4 | |||
| PTPN22 | NM_001308297.2 | c.757-34G>T | intron | N/A | NP_001295226.2 | F5H2S8 | |||
| PTPN22 | NM_001193431.3 | c.829-34G>T | intron | N/A | NP_001180360.2 |
Ensembl Transcripts
| Sel. | Gene | Transcript | Tags | HGVSc | HGVSp | Effect | Exon Rank | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|---|
| PTPN22 | ENST00000359785.10 | TSL:1 MANE Select | c.829-34G>T | intron | N/A | ENSP00000352833.5 | A0A0B4J1S7 | ||
| PTPN22 | ENST00000420377.6 | TSL:1 | c.829-34G>T | intron | N/A | ENSP00000388229.2 | E9PMT0 | ||
| PTPN22 | ENST00000538253.5 | TSL:1 | c.757-34G>T | intron | N/A | ENSP00000439372.2 | F5H2S8 |
Frequencies
GnomAD3 genomes 0.00 AC: 0AN: 151656Hom.: 0 Cov.: 32
GnomAD3 genomes
AF:
AC:
0
AN:
151656
Hom.:
Cov.:
32
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
GnomAD2 exomes AF: 0.0000363 AC: 8AN: 220260 AF XY: 0.0000416 show subpopulations
GnomAD2 exomes
AF:
AC:
8
AN:
220260
AF XY:
Gnomad AFR exome
AF:
Gnomad AMR exome
AF:
Gnomad ASJ exome
AF:
Gnomad EAS exome
AF:
Gnomad FIN exome
AF:
Gnomad NFE exome
AF:
Gnomad OTH exome
AF:
GnomAD4 exome AF: 0.0000126 AC: 18AN: 1423768Hom.: 0 Cov.: 28 AF XY: 0.0000184 AC XY: 13AN XY: 707870 show subpopulations ⚠️ The allele balance in gnomAD version 4 Exomes is significantly skewed from the expected value of 0.5.
GnomAD4 exome
AF:
AC:
18
AN:
1423768
Hom.:
Cov.:
28
AF XY:
AC XY:
13
AN XY:
707870
show subpopulations
⚠️ The allele balance in gnomAD version 4 Exomes is significantly skewed from the expected value of 0.5.
African (AFR)
AF:
AC:
2
AN:
31124
American (AMR)
AF:
AC:
4
AN:
34686
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
24512
East Asian (EAS)
AF:
AC:
0
AN:
39392
South Asian (SAS)
AF:
AC:
1
AN:
81210
European-Finnish (FIN)
AF:
AC:
0
AN:
50814
Middle Eastern (MID)
AF:
AC:
0
AN:
5566
European-Non Finnish (NFE)
AF:
AC:
10
AN:
1097792
Other (OTH)
AF:
AC:
1
AN:
58672
⚠️ The allele balance in gnomAD4 Exomes is highly skewed from 0.5 (p-value = 0), which strongly suggests a high chance of mosaicism in these individuals.
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.278
Heterozygous variant carriers
0
2
4
6
8
10
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Age Distribution
Exome Het
Variant carriers
0
2
4
6
8
10
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
GnomAD4 genome 0.00 AC: 0AN: 151656Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74026
GnomAD4 genome
Data not reliable, filtered out with message: AC0;AS_VQSR
AF:
AC:
0
AN:
151656
Hom.:
Cov.:
32
AF XY:
AC XY:
0
AN XY:
74026
African (AFR)
AF:
AC:
0
AN:
41298
American (AMR)
AF:
AC:
0
AN:
15248
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
3468
East Asian (EAS)
AF:
AC:
0
AN:
5192
South Asian (SAS)
AF:
AC:
0
AN:
4814
European-Finnish (FIN)
AF:
AC:
0
AN:
10450
Middle Eastern (MID)
AF:
AC:
0
AN:
316
European-Non Finnish (NFE)
AF:
AC:
0
AN:
67876
Other (OTH)
AF:
AC:
0
AN:
2086
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
DANN
Benign
PhyloP100
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.