Variant rs2295136 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_007039.4(PTPN21):c.3397-93C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.382 in 1,279,722 control chromosomes in the GnomAD database, including 96,200 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 0.35 ( 9858 hom., cov: 32)

Exomes 𝑓: 0.39 ( 86342 hom. )

Consequence

PTPN21
NM_007039.4 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.744

Variant links:

Genes affected

PTPN21 (HGNC:9651): (protein tyrosine phosphatase non-receptor type 21) 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 N-terminal domain, similar to cytoskeletal- associated proteins including band 4.1, ezrin, merlin, and radixin. This PTP was shown to specially interact with BMX/ETK, a member of Tec tyrosine kinase family characterized by a multimodular structures including PH, SH3, and SH2 domains. The interaction of this PTP with BMX kinase was found to increase the activation of STAT3, but not STAT2 kinase. Studies of the similar gene in mice suggested the possible roles of this PTP in liver regeneration and spermatogenesis. [provided by RefSeq, Jul 2008]

PTPN21 links:

PTPN21 (HGNC:):

PTPN21 links:

SPATA7 (HGNC:20423): (spermatogenesis associated 7) This gene, originally isolated from testis, is also expressed in retina. Mutations in this gene are associated with Leber congenital amaurosis and juvenile retinitis pigmentosa. Alternatively spliced transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, May 2010]

SPATA7 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.92).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.402 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
PTPN21	NM_007039.4 linkuse as main transcript	c.3397-93C>T		intron_variant		ENST00000556564.6	NP_008970.2	Q16825

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
PTPN21	ENST00000556564.6 linkuse as main transcript	c.3397-93C>T		intron_variant		1	NM_007039.4	ENSP00000452414.1		Q16825

Frequencies

GnomAD3 genomes

AF:

0.352

AC:

53452

AN:

151948

Hom.:

9863

Cov.:

show subpopulations

Gnomad AFR

AF:

0.304

Gnomad AMI

AF:

0.424

Gnomad AMR

AF:

0.259

Gnomad ASJ

AF:

0.467

Gnomad EAS

AF:

0.187

Gnomad SAS

AF:

0.265

Gnomad FIN

AF:

0.391

Gnomad MID

AF:

0.418

Gnomad NFE

AF:

0.406

Gnomad OTH

AF:

0.377

GnomAD4 exome

AF:

0.387

AC:

436002

AN:

1127656

Hom.:

86342

AF XY:

0.384

AC XY:

215757

AN XY:

561632

show subpopulations

Gnomad4 AFR exome

AF:

0.303

Gnomad4 AMR exome

AF:

0.200

Gnomad4 ASJ exome

AF:

0.476

Gnomad4 EAS exome

AF:

0.175

Gnomad4 SAS exome

AF:

0.264

Gnomad4 FIN exome

AF:

0.382

Gnomad4 NFE exome

AF:

0.410

Gnomad4 OTH exome

AF:

0.384

GnomAD4 genome

AF:

0.352

AC:

53452

AN:

152066

Hom.:

9858

Cov.:

AF XY:

0.346

AC XY:

25725

AN XY:

74338

show subpopulations

Gnomad4 AFR

AF:

0.304

Gnomad4 AMR

AF:

0.258

Gnomad4 ASJ

AF:

0.467

Gnomad4 EAS

AF:

0.187

Gnomad4 SAS

AF:

0.265

Gnomad4 FIN

AF:

0.391

Gnomad4 NFE

AF:

0.406

Gnomad4 OTH

AF:

0.373

Alfa

AF:

0.388

Hom.:

16342

Bravo

AF:

0.341

Asia WGS

AF:

0.213

AC:

743

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.92

CADD

Benign

7.3

DANN

Benign

0.53

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

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over