chr1-113831813-C-T

Position:

• chr1-113831813-C-T

Variant summary

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

The ENST00000359785.10(PTPN22):​c.2053+1298G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.767 in 152,182 control chromosomes in the GnomAD database, including 45,681 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 (45681 hom., cov: 32)
• Consequence: PTPN22 ENST00000359785.10 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.240

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=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.893 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
PTPN22	NM_015967.8	c.2053+1298G>A		intron_variant		ENST00000359785.10	NP_057051.4
PTPN22	XM_047417630.1	c.1903+1298G>A		intron_variant			XP_047273586.1
AP4B1-AS1	NR_125965.1	n.414+16341C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
PTPN22	ENST00000359785.10	c.2053+1298G>A		intron_variant		1	NM_015967.8	ENSP00000352833	P1
	ENST00000664434.1	n.470C>T		splice_region_variant, non_coding_transcript_exon_variant	4/6

Frequencies

GnomAD3 genomes AF: 0.767 AC: 116590 AN: 152064 Hom.: 45627 Cov.: 32

Gnomad AFR AF: 0.900

Gnomad AMI AF: 0.820

Gnomad AMR AF: 0.641

Gnomad ASJ AF: 0.762

Gnomad EAS AF: 0.390

Gnomad SAS AF: 0.770

Gnomad FIN AF: 0.687

Gnomad MID AF: 0.722

Gnomad NFE AF: 0.755

Gnomad OTH AF: 0.742

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

GnomAD4 genome AF: 0.767 AC: 116705 AN: 152182 Hom.: 45681 Cov.: 32 AF XY: 0.760 AC XY: 56555 AN XY: 74398

Gnomad4 AFR AF: 0.900

Gnomad4 AMR AF: 0.641

Gnomad4 ASJ AF: 0.762

Gnomad4 EAS AF: 0.390

Gnomad4 SAS AF: 0.770

Gnomad4 FIN AF: 0.687

Gnomad4 NFE AF: 0.755

Gnomad4 OTH AF: 0.742

Alfa AF: 0.749 Hom.: 46376

Bravo AF: 0.762

Asia WGS AF: 0.637 AC: 2218 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.46
DANN	Benign	0.32

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: rs1217395; hg19: chr1-114374435;