dbSNP rs913275: PTPA:c.*901G>A (chr9-129148365-G-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_178000.3(PTPA):c.*901G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.591 in 152,752 control chromosomes in the GnomAD database, including 28,767 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 0.59 ( 28611 hom., cov: 34)

Exomes 𝑓: 0.67 ( 156 hom. )

Consequence

PTPA
NM_178000.3 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -2.15

Publications

20 publications found

Variant links:

Genes affected

PTPA (HGNC:9308): (protein phosphatase 2 phosphatase activator) Protein phosphatase 2A is one of the four major Ser/Thr phosphatases and is implicated in the negative control of cell growth and division. Protein phosphatase 2A holoenzymes are heterotrimeric proteins composed of a structural subunit A, a catalytic subunit C, and a regulatory subunit B. The regulatory subunit is encoded by a diverse set of genes that have been grouped into the B/PR55, B'/PR61, and B''/PR72 families. These different regulatory subunits confer distinct enzymatic specificities and intracellular localizations to the holozenzyme. The product of this gene belongs to the B' family. This gene encodes a specific phosphotyrosyl phosphatase activator of the dimeric form of protein phosphatase 2A. Alternative splicing results in multiple transcript variants encoding different isoforms. [provided by RefSeq, Jul 2008]

PTPA links:

ENSG00000235007 (HGNC:):

ENSG00000235007 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=-0.88).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.697 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PTPA	NM_178000.3 link	c.*901G>A		3_prime_UTR_variant	Exon 10 of 10	ENST00000393370.7	NP_821067.1	Q15257-2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PTPA	ENST00000393370.7 link	c.*901G>A		3_prime_UTR_variant	Exon 10 of 10	1	NM_178000.3	ENSP00000377036.2		Q15257-2
ENSG00000235007	ENST00000674648.1 link	c.108+5813G>A		intron_variant	Intron 2 of 2			ENSP00000502744.1		A0A6Q8PH23

Frequencies

GnomAD3 genomes

AF:

0.591

AC:

89826

AN:

151960

Hom.:

28613

Cov.:

show subpopulations

Gnomad AFR

AF:

0.336

Gnomad AMI

AF:

0.601

Gnomad AMR

AF:

0.599

Gnomad ASJ

AF:

0.713

Gnomad EAS

AF:

0.579

Gnomad SAS

AF:

0.682

Gnomad FIN

AF:

0.784

Gnomad MID

AF:

0.630

Gnomad NFE

AF:

0.702

Gnomad OTH

AF:

0.602

GnomAD4 exome

AF:

0.671

AC:

452

AN:

674

Hom.:

156

Cov.:

AF XY:

0.655

AC XY:

249

AN XY:

380

show subpopulations

African (AFR)

AF:

0.222

AC:

AN:

American (AMR)

AF:

0.500

AC:

AN:

Ashkenazi Jewish (ASJ)

AF:

1.00

AC:

AN:

East Asian (EAS)

AF:

0.590

AC:

AN:

South Asian (SAS)

AF:

0.500

AC:

AN:

European-Finnish (FIN)

AF:

0.704

AC:

AN:

Middle Eastern (MID)

AF:

0.500

AC:

AN:

European-Non Finnish (NFE)

AF:

0.700

AC:

318

AN:

454

Other (OTH)

AF:

0.625

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.513

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

<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:

0.591

AC:

89857

AN:

152078

Hom.:

28611

Cov.:

AF XY:

0.597

AC XY:

44426

AN XY:

74364

show subpopulations

African (AFR)

AF:

0.336

AC:

13917

AN:

41466

American (AMR)

AF:

0.599

AC:

9159

AN:

15288

Ashkenazi Jewish (ASJ)

AF:

0.713

AC:

2477

AN:

3472

East Asian (EAS)

AF:

0.578

AC:

2983

AN:

5160

South Asian (SAS)

AF:

0.683

AC:

3300

AN:

4830

European-Finnish (FIN)

AF:

0.784

AC:

8313

AN:

10598

Middle Eastern (MID)

AF:

0.629

AC:

185

AN:

294

European-Non Finnish (NFE)

AF:

0.702

AC:

47711

AN:

67954

Other (OTH)

AF:

0.601

AC:

1264

AN:

2104

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

1732

3464

5195

6927

8659

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

740

1480

2220

2960

3700

<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:

0.653

Hom.:

14432

Bravo

AF:

0.563

Asia WGS

AF:

0.583

AC:

2030

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.88

CADD

Benign

0.094

(source)

DANN

Benign

0.53

PhyloP100

-2.1

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.3

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

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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