rs7786808

Variant names:

• chr7-158430414-A-G
• rs7786808
• NM_002847.5:c.163+59321T>C

Variant summary

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

The NM_002847.5(PTPRN2):​c.163+59321T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.585 in 152,058 control chromosomes in the GnomAD database, including 26,529 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 0.59 (26529 hom., cov: 33)
• Consequence: PTPRN2 NM_002847.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.38
• Publications: 10 publications found

Genes affected

PTPRN2 (HGNC:9677): (protein tyrosine phosphatase receptor type N2) This gene encodes a protein with sequence similarity to receptor-like protein tyrosine phosphatases. However, tyrosine phosphatase activity has not been experimentally validated for this protein. Studies of the rat ortholog suggest that the encoded protein may instead function as a phosphatidylinositol phosphatase with the ability to dephosphorylate phosphatidylinositol 3-phosphate and phosphatidylinositol 4,5-diphosphate, and this function may be involved in the regulation of insulin secretion. This protein has been identified as an autoantigen in insulin-dependent diabetes mellitus. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Feb 2015]

ACMG classification

Our verdict: Benign. The variant received -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 = 0.646 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PTPRN2	NM_002847.5	c.163+59321T>C		intron_variant	Intron 2 of 22	ENST00000389418.9	NP_002838.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PTPRN2	ENST00000389418.9	c.163+59321T>C		intron_variant	Intron 2 of 22	1	NM_002847.5	ENSP00000374069.4
PTPRN2	ENST00000389416.8	c.113-113482T>C		intron_variant	Intron 1 of 21	1		ENSP00000374067.4
PTPRN2	ENST00000389413.7	c.163+59321T>C		intron_variant	Intron 2 of 21	1		ENSP00000374064.3
PTPRN2	ENST00000409483.5	c.163+59321T>C		intron_variant	Intron 2 of 21	2		ENSP00000387114.1

Frequencies

GnomAD3 genomes AF: 0.585 AC: 88926 AN: 151940 Hom.: 26510 Cov.: 33

Gnomad AFR AF: 0.652

Gnomad AMI AF: 0.725

Gnomad AMR AF: 0.496

Gnomad ASJ AF: 0.576

Gnomad EAS AF: 0.358

Gnomad SAS AF: 0.575

Gnomad FIN AF: 0.531

Gnomad MID AF: 0.509

Gnomad NFE AF: 0.591

Gnomad OTH AF: 0.568

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

GnomAD4 genome AF: 0.585 AC: 88999 AN: 152058 Hom.: 26529 Cov.: 33 AF XY: 0.579 AC XY: 43022 AN XY: 74318

African (AFR) AF: 0.652 AC: 27063 AN: 41506

American (AMR) AF: 0.496 AC: 7578 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.576 AC: 2000 AN: 3472

East Asian (EAS) AF: 0.358 AC: 1838 AN: 5132

South Asian (SAS) AF: 0.574 AC: 2764 AN: 4816

European-Finnish (FIN) AF: 0.531 AC: 5607 AN: 10568

Middle Eastern (MID) AF: 0.524 AC: 154 AN: 294

European-Non Finnish (NFE) AF: 0.591 AC: 40140 AN: 67964

Other (OTH) AF: 0.568 AC: 1197 AN: 2106

Alfa AF: 0.584 Hom.: 68142

Bravo AF: 0.579

Asia WGS AF: 0.506 AC: 1763 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	0.064
DANN	Benign	0.34
PhyloP100		-1.4
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: rs7786808; hg19: chr7-158223106;