rs1178032

Positions:

• chr20-3001875-C-T

Variant summary

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

The NM_001385305.1(PTPRA):​c.739-3181C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.242 in 152,120 control chromosomes in the GnomAD database, including 7,919 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 0.24 (7919 hom., cov: 32)
• Consequence: PTPRA NM_001385305.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.139

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=-0.85).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.573 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
PTPRA	NM_001385305.1	c.739-3181C>T		intron_variant		ENST00000399903.7	NP_001372234.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
PTPRA	ENST00000399903.7	c.739-3181C>T		intron_variant		5	NM_001385305.1	ENSP00000382787	P4

Frequencies

GnomAD3 genomes AF: 0.242 AC: 36775 AN: 152002 Hom.: 7909 Cov.: 32

Gnomad AFR AF: 0.580

Gnomad AMI AF: 0.0998

Gnomad AMR AF: 0.197

Gnomad ASJ AF: 0.0922

Gnomad EAS AF: 0.123

Gnomad SAS AF: 0.0949

Gnomad FIN AF: 0.0911

Gnomad MID AF: 0.0633

Gnomad NFE AF: 0.102

Gnomad OTH AF: 0.187

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

GnomAD4 genome AF: 0.242 AC: 36818 AN: 152120 Hom.: 7919 Cov.: 32 AF XY: 0.236 AC XY: 17557 AN XY: 74366

Gnomad4 AFR AF: 0.580

Gnomad4 AMR AF: 0.196

Gnomad4 ASJ AF: 0.0922

Gnomad4 EAS AF: 0.123

Gnomad4 SAS AF: 0.0956

Gnomad4 FIN AF: 0.0911

Gnomad4 NFE AF: 0.102

Gnomad4 OTH AF: 0.184

Alfa AF: 0.182 Hom.: 776

Bravo AF: 0.266

Asia WGS AF: 0.120 AC: 416 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	6.7
DANN	Benign	0.44

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: rs1178032; hg19: chr20-2982521;