chr1-113821854-G-A

Variant names:

• chr1-113821854-G-A
• rs1217388
• NM_015967.8:c.2282-2200C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_015967.8(PTPN22):​c.2282-2200C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.768 in 152,102 control chromosomes in the GnomAD database, including 45,736 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 0.77 (45736 hom., cov: 31)
• Consequence: PTPN22 NM_015967.8 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.142
• Publications: 24 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]

AP4B1-AS1 (HGNC:44114): (AP4B1 antisense RNA 1)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.63).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.893 is higher than 0.05.

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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PTPN22	NM_015967.8	MANE Select	c.2282-2200C>T		intron	N/A	NP_057051.4
	PTPN22	NM_001308297.2		c.2210-2200C>T		intron	N/A	NP_001295226.2
	PTPN22	NM_001193431.3		c.2198-2200C>T		intron	N/A	NP_001180360.2

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PTPN22	ENST00000359785.10	TSL:1 MANE Select	c.2282-2200C>T		intron	N/A	ENSP00000352833.5
	PTPN22	ENST00000420377.6	TSL:1	c.2282-2200C>T		intron	N/A	ENSP00000388229.2
	PTPN22	ENST00000538253.5	TSL:1	c.2210-2200C>T		intron	N/A	ENSP00000439372.2

Frequencies

GnomAD3 genomes AF: 0.767 AC: 116632 AN: 151984 Hom.: 45682 Cov.: 31

Gnomad AFR AF: 0.900

Gnomad AMI AF: 0.817

Gnomad AMR AF: 0.641

Gnomad ASJ AF: 0.763

Gnomad EAS AF: 0.390

Gnomad SAS AF: 0.770

Gnomad FIN AF: 0.686

Gnomad MID AF: 0.723

Gnomad NFE AF: 0.756

Gnomad OTH AF: 0.744

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.768 AC: 116747 AN: 152102 Hom.: 45736 Cov.: 31 AF XY: 0.761 AC XY: 56562 AN XY: 74330

African (AFR) AF: 0.900 AC: 37397 AN: 41532

American (AMR) AF: 0.641 AC: 9782 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.763 AC: 2645 AN: 3466

East Asian (EAS) AF: 0.390 AC: 2020 AN: 5174

South Asian (SAS) AF: 0.770 AC: 3706 AN: 4812

European-Finnish (FIN) AF: 0.686 AC: 7246 AN: 10560

Middle Eastern (MID) AF: 0.733 AC: 214 AN: 292

European-Non Finnish (NFE) AF: 0.756 AC: 51430 AN: 67994

Other (OTH) AF: 0.743 AC: 1567 AN: 2108

Alfa AF: 0.754 Hom.: 68923

Bravo AF: 0.762

Asia WGS AF: 0.638 AC: 2219 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.63
CADD	Benign	6.0
DANN	Benign	0.81
PhyloP100		-0.14
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs1217388; hg19: chr1-114364476;