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:

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:

ENSG00000289911 (HGNC:):

ENSG00000289911 links:

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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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001385255.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

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

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
PTP4A1	ENST00000639568.2	TSL:5	c.-565A>C	5_prime_UTR	Exon 3 of 4	ENSP00000497431.1
PTP4A1	ENST00000648894.1		c.-446+17844A>C	intron	N/A	ENSP00000497588.1
PTP4A1	ENST00000470661.1	TSL:2	n.332+22290A>C	intron	N/A

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 v4.9

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

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over