Genetic Variant PTP4A1:c.-711-2718T>C (chr6-63525101-T-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_001385254.1(PTP4A1):c.-711-2718T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.535 in 152,028 control chromosomes in the GnomAD database, including 23,622 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 0.54 ( 23622 hom., cov: 32)

Consequence

PTP4A1
NM_001385254.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.393

Publications

3 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=-0.85).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.765 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001385254.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	HGVSc	Effect	Exon Rank	Protein	UniProt
PTP4A1	NM_001385254.1	c.-711-2718T>C	intron	N/A	NP_001372183.1	Q93096
PTP4A1	NM_001385255.1	c.-905-2718T>C	intron	N/A	NP_001372184.1	Q93096
PTP4A1	NM_001385256.1	c.-905-2718T>C	intron	N/A	NP_001372185.1	Q93096

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
PTP4A1	ENST00000648894.1		c.-905-2718T>C	intron	N/A	ENSP00000497588.1	Q93096
PTP4A1	ENST00000639568.2	TSL:5	c.-905-2718T>C	intron	N/A	ENSP00000497431.1	A0A3B3ISR8
PTP4A1	ENST00000470661.1	TSL:2	n.67-2718T>C	intron	N/A

Frequencies

GnomAD3 genomes

AF:

0.535

AC:

81232

AN:

151910

Hom.:

23559

Cov.:

show subpopulations

Gnomad AFR

AF:

0.772

Gnomad AMI

AF:

0.544

Gnomad AMR

AF:

0.532

Gnomad ASJ

AF:

0.359

Gnomad EAS

AF:

0.449

Gnomad SAS

AF:

0.482

Gnomad FIN

AF:

0.382

Gnomad MID

AF:

0.449

Gnomad NFE

AF:

0.436

Gnomad OTH

AF:

0.493

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

GnomAD4 genome

AF:

0.535

AC:

81362

AN:

152028

Hom.:

23622

Cov.:

AF XY:

0.531

AC XY:

39445

AN XY:

74300

show subpopulations

African (AFR)

AF:

0.772

AC:

32033

AN:

41492

American (AMR)

AF:

0.533

AC:

8127

AN:

15254

Ashkenazi Jewish (ASJ)

AF:

0.359

AC:

1243

AN:

3466

East Asian (EAS)

AF:

0.449

AC:

2322

AN:

5168

South Asian (SAS)

AF:

0.484

AC:

2332

AN:

4818

European-Finnish (FIN)

AF:

0.382

AC:

4033

AN:

10556

Middle Eastern (MID)

AF:

0.459

AC:

135

AN:

294

European-Non Finnish (NFE)

AF:

0.436

AC:

29603

AN:

67968

Other (OTH)

AF:

0.494

AC:

1039

AN:

2102

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

1765

3530

5296

7061

8826

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

682

1364

2046

2728

3410

<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:

0.500

Hom.:

3396

Bravo

AF:

0.557

Asia WGS

AF:

0.452

AC:

1569

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

0.79

(source)

DANN

Benign

0.48

PhyloP100

-0.39

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