dbSNP rs1178032: PTPRA:c.739-3181C>T (chr20-3001875-C-T) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The NM_001385305.1(PTPRA):c.739-3181C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.242 in 152,120 control chromosomes in the GnomAD database, including 7,919 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 0.24 ( 7919 hom., cov: 32)

Consequence

PTPRA
NM_001385305.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.139

Publications

6 publications found

Variant links:

Genes affected

PTPRA (HGNC:9664): (protein tyrosine phosphatase receptor type A) 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 contains an extracellular domain, a single transmembrane segment and two tandem intracytoplasmic catalytic domains, and thus represents a receptor-type PTP. This PTP has been shown to dephosphorylate and activate Src family tyrosine kinases, and is implicated in the regulation of integrin signaling, cell adhesion and proliferation. Three alternatively spliced variants of this gene, which encode two distinct isoforms, have been reported. [provided by RefSeq, Jul 2008]

PTPRA 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=-0.85).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.573 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001385305.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
PTPRA	NM_001385305.1	MANE Select	c.739-3181C>T	intron	N/A	NP_001372234.1	P18433-5
PTPRA	NM_001385302.1		c.772-3181C>T	intron	N/A	NP_001372231.1	B7Z2A4
PTPRA	NM_001385303.1		c.772-3181C>T	intron	N/A	NP_001372232.1	B7Z2A4

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
PTPRA	ENST00000399903.7	TSL:5 MANE Select	c.739-3181C>T	intron	N/A	ENSP00000382787.2	P18433-5
PTPRA	ENST00000216877.10	TSL:1	c.712-3181C>T	intron	N/A	ENSP00000216877.6	P18433-6
PTPRA	ENST00000356147.3	TSL:1	c.712-3181C>T	intron	N/A	ENSP00000348468.3	P18433-6

Frequencies

GnomAD3 genomes

AF:

0.242

AC:

36775

AN:

152002

Hom.:

7909

Cov.:

show subpopulations

Gnomad AFR

AF:

0.580

Gnomad AMI

AF:

0.0998

Gnomad AMR

AF:

0.197

Gnomad ASJ

AF:

0.0922

Gnomad EAS

AF:

0.123

Gnomad SAS

AF:

0.0949

Gnomad FIN

AF:

0.0911

Gnomad MID

AF:

0.0633

Gnomad NFE

AF:

0.102

Gnomad OTH

AF:

0.187

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

GnomAD4 genome

AF:

0.242

AC:

36818

AN:

152120

Hom.:

7919

Cov.:

AF XY:

0.236

AC XY:

17557

AN XY:

74366

show subpopulations

African (AFR)

AF:

0.580

AC:

24024

AN:

41454

American (AMR)

AF:

0.196

AC:

3000

AN:

15288

Ashkenazi Jewish (ASJ)

AF:

0.0922

AC:

320

AN:

3470

East Asian (EAS)

AF:

0.123

AC:

635

AN:

5182

South Asian (SAS)

AF:

0.0956

AC:

461

AN:

4820

European-Finnish (FIN)

AF:

0.0911

AC:

965

AN:

10594

Middle Eastern (MID)

AF:

0.0646

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.102

AC:

6915

AN:

68000

Other (OTH)

AF:

0.184

AC:

388

AN:

2106

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

1080

2159

3239

4318

5398

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

322

644

966

1288

1610

<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:

0.182

Hom.:

776

Bravo

AF:

0.266

Asia WGS

AF:

0.120

AC:

416

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.85

CADD

Benign

6.7

(source)

DANN

Benign

0.44

PhyloP100

0.14

Mutation Taster

=100/0

polymorphism (auto)

(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

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over