rs1638742

Variant names:

• chr7-157745860-T-C
• rs1638742
• NM_002847.5:c.1789-62923A>G

Variant summary

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

The ENST00000389418.9(PTPRN2):​c.1789-62923A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.114 in 152,112 control chromosomes in the GnomAD database, including 1,204 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 0.11 (1204 hom., cov: 33)
• Consequence: PTPRN2 ENST00000389418.9 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.06
• Publications: 7 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=-0.99).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.202 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000389418.9. 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
	PTPRN2	NM_002847.5	MANE Select	c.1789-62923A>G		intron	N/A	NP_002838.2
	PTPRN2	NM_001308268.2		c.1858-62923A>G		intron	N/A	NP_001295197.1
	PTPRN2	NM_130842.4		c.1738-62923A>G		intron	N/A	NP_570857.2

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PTPRN2	ENST00000389418.9	TSL:1 MANE Select	c.1789-62923A>G		intron	N/A	ENSP00000374069.4
	PTPRN2	ENST00000389416.8	TSL:1	c.1738-62923A>G		intron	N/A	ENSP00000374067.4
	PTPRN2	ENST00000389413.7	TSL:1	c.1702-62923A>G		intron	N/A	ENSP00000374064.3

Frequencies

GnomAD3 genomes AF: 0.114 AC: 17330 AN: 151994 Hom.: 1189 Cov.: 33

Gnomad AFR AF: 0.141

Gnomad AMI AF: 0.0592

Gnomad AMR AF: 0.207

Gnomad ASJ AF: 0.115

Gnomad EAS AF: 0.162

Gnomad SAS AF: 0.133

Gnomad FIN AF: 0.0758

Gnomad MID AF: 0.104

Gnomad NFE AF: 0.0779

Gnomad OTH AF: 0.121

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

GnomAD4 genome AF: 0.114 AC: 17372 AN: 152112 Hom.: 1204 Cov.: 33 AF XY: 0.117 AC XY: 8690 AN XY: 74380

African (AFR) AF: 0.142 AC: 5869 AN: 41452

American (AMR) AF: 0.208 AC: 3183 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.115 AC: 398 AN: 3468

East Asian (EAS) AF: 0.161 AC: 833 AN: 5176

South Asian (SAS) AF: 0.135 AC: 649 AN: 4824

European-Finnish (FIN) AF: 0.0758 AC: 805 AN: 10620

Middle Eastern (MID) AF: 0.105 AC: 31 AN: 294

European-Non Finnish (NFE) AF: 0.0779 AC: 5298 AN: 67980

Other (OTH) AF: 0.119 AC: 252 AN: 2112

Alfa AF: 0.101 Hom.: 1822

Bravo AF: 0.128

Asia WGS AF: 0.135 AC: 469 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.81
DANN	Benign	0.14
PhyloP100		-1.1
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: rs1638742; hg19: chr7-157538552;