rs600832

chr20-2893440-C-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001385305.1(PTPRA):c.-129+19680C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.667 in 152,092 control chromosomes in the GnomAD database, including 35,357 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 0.67 (35357 hom., cov: 32)
• Consequence: PTPRA NM_001385305.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.136

Genes affected

PTPRA (HGNC:9664): (protein tyrosine phosphatase receptor type A) 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 extracellular domain, a single transmembrane segment and two tandem intracytoplasmic catalytic domains, and thus represents a receptor-type PTP. This PTP has been shown to dephosphorylate and activate Src family tyrosine kinases, and is implicated in the regulation of integrin signaling, cell adhesion and proliferation. Three alternatively spliced variants of this gene, which encode two distinct isoforms, have been reported. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.839 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PTPRA	NM_001385305.1	c.-129+19680C>G		intron_variant		ENST00000399903.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PTPRA	ENST00000399903.7	c.-129+19680C>G		intron_variant		5	NM_001385305.1	P4

Frequencies

GnomAD3 genomes AF: 0.667 AC: 101404 AN: 151974 Hom.: 35301 Cov.: 32

Gnomad AFR AF: 0.846

Gnomad AMI AF: 0.582

Gnomad AMR AF: 0.716

Gnomad ASJ AF: 0.509

Gnomad EAS AF: 0.858

Gnomad SAS AF: 0.777

Gnomad FIN AF: 0.561

Gnomad MID AF: 0.563

Gnomad NFE AF: 0.551

Gnomad OTH AF: 0.659

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

GnomAD4 genome AF: 0.667 AC: 101521 AN: 152092 Hom.: 35357 Cov.: 32 AF XY: 0.673 AC XY: 50044 AN XY: 74354

Gnomad4 AFR AF: 0.847

Gnomad4 AMR AF: 0.716

Gnomad4 ASJ AF: 0.509

Gnomad4 EAS AF: 0.858

Gnomad4 SAS AF: 0.775

Gnomad4 FIN AF: 0.561

Gnomad4 NFE AF: 0.551

Gnomad4 OTH AF: 0.660

Alfa AF: 0.615 Hom.: 3699

Bravo AF: 0.686

Asia WGS AF: 0.801 AC: 2785 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
Cadd	Benign	3.4
Dann	Benign	0.37

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

Other links and lift over

dbSNP: rs600832; hg19: chr20-2874086;