NM_002847.5:c.*32C>T

Variant names:

• chr7-157540682-G-A
• rs1122307
• NM_002847.5:c.*32C>T

Variant summary

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

The NM_002847.5(PTPRN2):​c.*32C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0809 in 1,484,268 control chromosomes in the GnomAD database, including 5,156 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 0.076 (475 hom., cov: 33)
  • Exomes 𝑓: 0.081 (4681 hom.)
• Consequence: PTPRN2 NM_002847.5 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0420
• Publications: 8 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=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.139 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PTPRN2	NM_002847.5	c.*32C>T		3_prime_UTR_variant	Exon 23 of 23	ENST00000389418.9	NP_002838.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PTPRN2	ENST00000389418.9	c.*32C>T		3_prime_UTR_variant	Exon 23 of 23	1	NM_002847.5	ENSP00000374069.4

Frequencies

GnomAD3 genomes AF: 0.0761 AC: 11573 AN: 152122 Hom.: 475 Cov.: 33

Gnomad AFR AF: 0.0559

Gnomad AMI AF: 0.00219

Gnomad AMR AF: 0.106

Gnomad ASJ AF: 0.0441

Gnomad EAS AF: 0.149

Gnomad SAS AF: 0.0860

Gnomad FIN AF: 0.0792

Gnomad MID AF: 0.0601

Gnomad NFE AF: 0.0781

Gnomad OTH AF: 0.0617

GnomAD2 exomes AF: 0.0874 AC: 13466 AN: 154076 AF XY: 0.0864

Gnomad AFR exome AF: 0.0562

Gnomad AMR exome AF: 0.115

Gnomad ASJ exome AF: 0.0415

Gnomad EAS exome AF: 0.148

Gnomad FIN exome AF: 0.0789

Gnomad NFE exome AF: 0.0803

Gnomad OTH exome AF: 0.0827

GnomAD4 exome AF: 0.0815 AC: 108554 AN: 1332028 Hom.: 4681 Cov.: 28 AF XY: 0.0819 AC XY: 54054 AN XY: 660366

African (AFR) AF: 0.0545 AC: 1633 AN: 29952

American (AMR) AF: 0.109 AC: 3822 AN: 34932

Ashkenazi Jewish (ASJ) AF: 0.0429 AC: 1059 AN: 24662

East Asian (EAS) AF: 0.139 AC: 4942 AN: 35538

South Asian (SAS) AF: 0.0821 AC: 6371 AN: 77614

European-Finnish (FIN) AF: 0.0747 AC: 3668 AN: 49078

Middle Eastern (MID) AF: 0.0479 AC: 266 AN: 5558

European-Non Finnish (NFE) AF: 0.0808 AC: 82292 AN: 1018856

Other (OTH) AF: 0.0806 AC: 4501 AN: 55838

GnomAD4 genome AF: 0.0761 AC: 11579 AN: 152240 Hom.: 475 Cov.: 33 AF XY: 0.0776 AC XY: 5777 AN XY: 74412

African (AFR) AF: 0.0558 AC: 2317 AN: 41560

American (AMR) AF: 0.106 AC: 1623 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.0441 AC: 153 AN: 3470

East Asian (EAS) AF: 0.148 AC: 764 AN: 5160

South Asian (SAS) AF: 0.0850 AC: 410 AN: 4822

European-Finnish (FIN) AF: 0.0792 AC: 840 AN: 10608

Middle Eastern (MID) AF: 0.0646 AC: 19 AN: 294

European-Non Finnish (NFE) AF: 0.0782 AC: 5316 AN: 68004

Other (OTH) AF: 0.0639 AC: 135 AN: 2112

Alfa AF: 0.0726 Hom.: 684

Bravo AF: 0.0771

Asia WGS AF: 0.105 AC: 365 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	0.31
DANN	Benign	0.52
PhyloP100		-0.042
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.040		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: rs1122307; hg19: chr7-157333376; COSMIC: COSV67021437;