Variant 7-157656369-G-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_StrongBP6_ModerateBP7BS2

The NM_002847.5(PTPRN2):c.2184C>A(p.Gly728=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0077 in 1,550,326 control chromosomes in the GnomAD database, including 61 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.0047 ( 6 hom., cov: 31)

Exomes 𝑓: 0.0080 ( 55 hom. )

Consequence

PTPRN2
NM_002847.5 synonymous

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 1.73

Variant links:

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]

PTPRN2 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -11 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.56).

BP6

Variant 7-157656369-G-T is Benign according to our data. Variant chr7-157656369-G-T is described in ClinVar as [Benign]. Clinvar id is 787541.Status of the report is criteria_provided_single_submitter, 1 stars.

BP7

Synonymous conserved (PhyloP=1.73 with no splicing effect.

BS2

High Homozygotes in GnomAd4 at 6 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PTPRN2	NM_002847.5 linkuse as main transcript	c.2184C>A	p.Gly728=	synonymous_variant	14/23	ENST00000389418.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PTPRN2	ENST00000389418.9 linkuse as main transcript	c.2184C>A	p.Gly728=	synonymous_variant	14/23	1	NM_002847.5	P2	Q92932-1
PTPRN2	ENST00000389416.8 linkuse as main transcript	c.2133C>A	p.Gly711=	synonymous_variant	13/22	1		A2	Q92932-4
PTPRN2	ENST00000389413.7 linkuse as main transcript	c.2097C>A	p.Gly699=	synonymous_variant	13/22	1			Q92932-2
PTPRN2	ENST00000409483.5 linkuse as main transcript	c.2070C>A	p.Gly690=	synonymous_variant	13/22	2

Frequencies

GnomAD3 genomes

AF:

0.00472

AC:

718

AN:

152088

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00152

Gnomad AMI

AF:

0.0175

Gnomad AMR

AF:

0.00242

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.000621

Gnomad FIN

AF:

0.00254

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.00832

Gnomad OTH

AF:

0.00287

GnomAD3 exomes

AF:

0.00425

AC:

665

AN:

156424

Hom.:

AF XY:

0.00441

AC XY:

363

AN XY:

82338

show subpopulations

Gnomad AFR exome

AF:

0.00124

Gnomad AMR exome

AF:

0.00234

Gnomad ASJ exome

AF:

0.000708

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.000964

Gnomad FIN exome

AF:

0.00391

Gnomad NFE exome

AF:

0.00807

Gnomad OTH exome

AF:

0.00497

GnomAD4 exome

AF:

0.00803

AC:

11225

AN:

1398120

Hom.:

Cov.:

AF XY:

0.00780

AC XY:

5375

AN XY:

689402

show subpopulations

Gnomad4 AFR exome

AF:

0.00145

Gnomad4 AMR exome

AF:

0.00190

Gnomad4 ASJ exome

AF:

0.000358

Gnomad4 EAS exome

AF:

0.0000280

Gnomad4 SAS exome

AF:

0.000946

Gnomad4 FIN exome

AF:

0.00469

Gnomad4 NFE exome

AF:

0.00969

Gnomad4 OTH exome

AF:

0.00599

GnomAD4 genome

AF:

0.00472

AC:

718

AN:

152206

Hom.:

Cov.:

AF XY:

0.00415

AC XY:

309

AN XY:

74386

show subpopulations

Gnomad4 AFR

AF:

0.00152

Gnomad4 AMR

AF:

0.00242

Gnomad4 ASJ

AF:

0.00

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.000622

Gnomad4 FIN

AF:

0.00254

Gnomad4 NFE

AF:

0.00832

Gnomad4 OTH

AF:

0.00284

Alfa

AF:

0.00304

Hom.:

Bravo

AF:

0.00461

Asia WGS

AF:

0.000866

AC:

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

Invitae

Dec 31, 2019

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.56

CADD

Benign

7.2

DANN

Benign

0.86

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over