dbSNP rs10943869: PTP4A1:c.-565A>C (chr6-63550374-A-C) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The NM_001385255.1(PTP4A1):c.-565A>C variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.253 in 151,952 control chromosomes in the GnomAD database, including 5,746 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 0.25 ( 5746 hom., cov: 31)

Exomes 𝑓: 0.0 ( 0 hom. )

Failed GnomAD Quality Control

Consequence

PTP4A1
NM_001385255.1 5_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.03

Publications

2 publications found

Variant links:

Genes affected

PTP4A1 (HGNC:9634): (protein tyrosine phosphatase 4A1) This gene encodes a member of a small class of prenylated protein tyrosine phosphatases (PTPs), which contain a PTP domain and a characteristic C-terminal prenylation motif. The encoded protein is a cell signaling molecule that plays regulatory roles in a variety of cellular processes, including cell proliferation and migration. The protein may also be involved in cancer development and metastasis. This tyrosine phosphatase is a nuclear protein, but may associate with plasma membrane by means of its prenylation motif. Pseudogenes related to this gene are located on chromosomes 1, 2, 5, 7, 11 and X. [provided by RefSeq, Jun 2013]

PTP4A1 links:

ENSG00000289911 (HGNC:):

ENSG00000289911 links:

LGSN (HGNC:21016): (lengsin, lens protein with glutamine synthetase domain) This gene encodes a protein with similarity to the GS I members of the glutamine synthetase superfamily. The encoded protein is referred to as a pseudo-glutamine synthetase because it has no glutamine synthesis activity and may function as a chaperone protein. This protein is localized to the lens and may be associated with cataract disease. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jan 2009]

LGSN 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=-0.65).

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.33 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank	Protein
PTP4A1	NM_001385255.1 link	c.-565A>C	5_prime_UTR_variant	Exon 4 of 9	NP_001372184.1
PTP4A1	NM_001385257.1 link	c.-565A>C	5_prime_UTR_variant	Exon 4 of 9	NP_001372186.1
PTP4A1	NM_001385258.1 link	c.-565A>C	5_prime_UTR_variant	Exon 4 of 9	NP_001372187.1

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL	Protein	UniProt
PTP4A1	ENST00000639568.2 link	c.-565A>C	5_prime_UTR_variant	Exon 3 of 4	5	ENSP00000497431.1	A0A3B3ISR8
PTP4A1	ENST00000648894.1 link	c.-446+17844A>C	intron_variant	Intron 3 of 7		ENSP00000497588.1	Q93096
PTP4A1	ENST00000470661.1 link	n.332+22290A>C	intron_variant	Intron 2 of 2	2

Frequencies

GnomAD3 genomes

AF:

0.253

AC:

38469

AN:

151834

Hom.:

5739

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0850

Gnomad AMI

AF:

0.410

Gnomad AMR

AF:

0.338

Gnomad ASJ

AF:

0.275

Gnomad EAS

AF:

0.250

Gnomad SAS

AF:

0.304

Gnomad FIN

AF:

0.246

Gnomad MID

AF:

0.306

Gnomad NFE

AF:

0.331

Gnomad OTH

AF:

0.277

GnomAD4 exome

Data not reliable, filtered out with message: AC0

AF:

0.00

AC:

AN:

Hom.:

Cov.:

AF XY:

0.00

AC XY:

AN XY:

African (AFR)

AC:

AN:

American (AMR)

AC:

AN:

Ashkenazi Jewish (ASJ)

AC:

AN:

East Asian (EAS)

AC:

AN:

South Asian (SAS)

AC:

AN:

European-Finnish (FIN)

AC:

AN:

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

0.00

AC:

AN:

Other (OTH)

AF:

0.00

AC:

AN:

GnomAD4 genome

AF:

0.253

AC:

38475

AN:

151952

Hom.:

5746

Cov.:

AF XY:

0.253

AC XY:

18782

AN XY:

74272

show subpopulations

African (AFR)

AF:

0.0848

AC:

3517

AN:

41472

American (AMR)

AF:

0.338

AC:

5149

AN:

15252

Ashkenazi Jewish (ASJ)

AF:

0.275

AC:

954

AN:

3470

East Asian (EAS)

AF:

0.250

AC:

1290

AN:

5166

South Asian (SAS)

AF:

0.307

AC:

1472

AN:

4800

European-Finnish (FIN)

AF:

0.246

AC:

2587

AN:

10530

Middle Eastern (MID)

AF:

0.312

AC:

AN:

292

European-Non Finnish (NFE)

AF:

0.331

AC:

22463

AN:

67948

Other (OTH)

AF:

0.274

AC:

579

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

1375

2750

4126

5501

6876

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

404

808

1212

1616

2020

<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:

0.294

Hom.:

1593

Bravo

AF:

0.253

Asia WGS

AF:

0.249

AC:

865

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.65

CADD

Benign

8.2

(source)

DANN

Benign

0.85

PhyloP100

1.0

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.1

Splicing

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

ClinVar

Computational scores

Splicing

Publications

Other links and lift over