Genetic Variant NM_007050.6:c.1561-77G>T (chr20-42352362-C-A) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_007050.6(PTPRT):c.1561-77G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.273 in 1,468,512 control chromosomes in the GnomAD database, including 59,170 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 0.23 ( 4753 hom., cov: 32)

Exomes 𝑓: 0.28 ( 54417 hom. )

Consequence

PTPRT
NM_007050.6 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.61

Publications

4 publications found

Variant links:

Genes affected

PTPRT (HGNC:9682): (protein tyrosine phosphatase receptor type T) The protein encoded by this gene is a member of the protein tyrosine phosphatase (PTP) family. PTPs are known to be signaling molecules that regulate a variety of cellular processes including cell growth, differentiation, mitotic cycle, and oncogenic transformation. This PTP possesses an extracellular region, a single transmembrane region, and two tandem intracellular catalytic domains, and thus represents a receptor-type PTP. The extracellular region contains a meprin-A5 antigen-PTP (MAM) domain, Ig-like and fibronectin type III-like repeats. The protein domain structure and the expression pattern of the mouse counterpart of this PTP suggest its roles in both signal transduction and cellular adhesion in the central nervous system. Two alternatively spliced transcript variants of this gene, which encode distinct proteins, have been reported. [provided by RefSeq, Jul 2008]

PTPRT links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.86).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.301 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PTPRT	NM_007050.6 link	c.1561-77G>T		intron_variant	Intron 9 of 30	ENST00000373187.6	NP_008981.4	O14522-3

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL	MANE	Protein	UniProt
PTPRT	ENST00000373187.6 link	c.1561-77G>T	intron_variant	Intron 9 of 30	1	NM_007050.6	ENSP00000362283.1	O14522-3
PTPRT	ENST00000373193.7 link	c.1561-77G>T	intron_variant	Intron 9 of 31	1		ENSP00000362289.4	O14522-1
PTPRT	ENST00000617474.1 link	n.*1419-77G>T	intron_variant	Intron 9 of 30	5		ENSP00000484248.1	A0A087X1J1

Frequencies

GnomAD3 genomes

AF:

0.226

AC:

34404

AN:

151980

Hom.:

4751

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0849

Gnomad AMI

AF:

0.180

Gnomad AMR

AF:

0.268

Gnomad ASJ

AF:

0.325

Gnomad EAS

AF:

0.0367

Gnomad SAS

AF:

0.100

Gnomad FIN

AF:

0.336

Gnomad MID

AF:

0.225

Gnomad NFE

AF:

0.305

Gnomad OTH

AF:

0.224

GnomAD4 exome

AF:

0.278

AC:

366374

AN:

1316414

Hom.:

54417

AF XY:

0.273

AC XY:

180088

AN XY:

659400

show subpopulations

African (AFR)

AF:

0.0804

AC:

2426

AN:

30184

American (AMR)

AF:

0.294

AC:

12699

AN:

43232

Ashkenazi Jewish (ASJ)

AF:

0.323

AC:

7885

AN:

24388

East Asian (EAS)

AF:

0.0718

AC:

2782

AN:

38744

South Asian (SAS)

AF:

0.112

AC:

9136

AN:

81304

European-Finnish (FIN)

AF:

0.331

AC:

16960

AN:

51254

Middle Eastern (MID)

AF:

0.230

AC:

1004

AN:

4366

European-Non Finnish (NFE)

AF:

0.303

AC:

299252

AN:

987580

Other (OTH)

AF:

0.257

AC:

14230

AN:

55362

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.506

Heterozygous variant carriers

12565

25130

37696

50261

62826

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

9188

18376

27564

36752

45940

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.226

AC:

34412

AN:

152098

Hom.:

4753

Cov.:

AF XY:

0.224

AC XY:

16662

AN XY:

74346

show subpopulations

African (AFR)

AF:

0.0851

AC:

3532

AN:

41502

American (AMR)

AF:

0.268

AC:

4099

AN:

15282

Ashkenazi Jewish (ASJ)

AF:

0.325

AC:

1129

AN:

3470

East Asian (EAS)

AF:

0.0366

AC:

189

AN:

5164

South Asian (SAS)

AF:

0.100

AC:

482

AN:

4808

European-Finnish (FIN)

AF:

0.336

AC:

3558

AN:

10576

Middle Eastern (MID)

AF:

0.214

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.305

AC:

20728

AN:

67976

Other (OTH)

AF:

0.221

AC:

468

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

1291

2582

3873

5164

6455

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

354

708

1062

1416

1770

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.269

Hom.:

11546

Bravo

AF:

0.218

Asia WGS

AF:

0.0910

AC:

317

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.86

CADD

Benign

0.30

(source)

DANN

Benign

0.34

PhyloP100

-1.6

Mutation Taster

=12/88

disease causing

(source)

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over