rs2476604

Positions:

• chr1-113863822-T-A
• chr1-113863822-T-G

Variant summary

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

The ENST00000359785.10(PTPN22):​c.88-4362A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.559 in 151,056 control chromosomes in the GnomAD database, including 24,342 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 0.56 (24342 hom., cov: 29)
• Consequence: PTPN22 ENST00000359785.10 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.00200

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)

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.633 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
PTPN22	NM_015967.8	c.88-4362A>T		intron_variant		ENST00000359785.10	NP_057051.4
PTPN22	XM_047417630.1	c.88-4362A>T		intron_variant			XP_047273586.1
AP4B1-AS1	NR_125965.1	n.415-34046T>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
PTPN22	ENST00000359785.10	c.88-4362A>T		intron_variant		1	NM_015967.8	ENSP00000352833	P1
AP4B1-AS1	ENST00000419536.1	n.246+5806T>A		intron_variant, non_coding_transcript_variant		2
	ENST00000664434.1	n.504+5806T>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.559 AC: 84354 AN: 150948 Hom.: 24321 Cov.: 29

Gnomad AFR AF: 0.638

Gnomad AMI AF: 0.585

Gnomad AMR AF: 0.451

Gnomad ASJ AF: 0.605

Gnomad EAS AF: 0.161

Gnomad SAS AF: 0.652

Gnomad FIN AF: 0.487

Gnomad MID AF: 0.580

Gnomad NFE AF: 0.567

Gnomad OTH AF: 0.548

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

GnomAD4 genome AF: 0.559 AC: 84422 AN: 151056 Hom.: 24342 Cov.: 29 AF XY: 0.553 AC XY: 40784 AN XY: 73744

Gnomad4 AFR AF: 0.638

Gnomad4 AMR AF: 0.451

Gnomad4 ASJ AF: 0.605

Gnomad4 EAS AF: 0.161

Gnomad4 SAS AF: 0.652

Gnomad4 FIN AF: 0.487

Gnomad4 NFE AF: 0.567

Gnomad4 OTH AF: 0.544

Alfa AF: 0.455 Hom.: 1314

Bravo AF: 0.551

Asia WGS AF: 0.432 AC: 1503 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	2.4
DANN	Benign	0.70

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: rs2476604; hg19: chr1-114406444;