1-113855490-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000359785.10(PTPN22):c.541-441G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.177 in 117,328 control chromosomes in the GnomAD database, including 1,783 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 0.18 (1783 hom., cov: 21)
• Consequence: PTPN22 ENST00000359785.10 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.738

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]

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.22 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PTPN22	NM_015967.8	c.541-441G>A		intron_variant		ENST00000359785.10
PTPN22	XM_047417630.1	c.469-441G>A		intron_variant
AP4B1-AS1	NR_125965.1	n.414+40018C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PTPN22	ENST00000359785.10	c.541-441G>A		intron_variant		1	NM_015967.8	P1
	ENST00000664434.1	n.471-2493C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.177 AC: 20783 AN: 117324 Hom.: 1783 Cov.: 21

Gnomad AFR AF: 0.104

Gnomad AMI AF: 0.228

Gnomad AMR AF: 0.219

Gnomad ASJ AF: 0.161

Gnomad EAS AF: 0.232

Gnomad SAS AF: 0.125

Gnomad FIN AF: 0.249

Gnomad MID AF: 0.189

Gnomad NFE AF: 0.195

Gnomad OTH AF: 0.186

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

GnomAD4 genome AF: 0.177 AC: 20781 AN: 117328 Hom.: 1783 Cov.: 21 AF XY: 0.181 AC XY: 9852 AN XY: 54430

Gnomad4 AFR AF: 0.104

Gnomad4 AMR AF: 0.219

Gnomad4 ASJ AF: 0.161

Gnomad4 EAS AF: 0.231

Gnomad4 SAS AF: 0.125

Gnomad4 FIN AF: 0.249

Gnomad4 NFE AF: 0.194

Gnomad4 OTH AF: 0.190

Alfa AF: 0.0625 Hom.: 80

Bravo AF: 0.152

Asia WGS AF: 0.192 AC: 667 AN: 3468

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
Cadd	Benign	0.86
Dann	Benign	0.46

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

Publications

LitVar

Other links and lift over

dbSNP: rs34122108; hg19: chr1-114398112;