20-3015777-T-A

Variant names:

• chr20-3015777-T-A
• rs1178015
• NM_001385305.1:c.907-72T>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001385305.1(PTPRA):​c.907-72T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.507 in 1,315,550 control chromosomes in the GnomAD database, including 172,990 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 0.53 (21645 hom., cov: 32)
  • Exomes 𝑓: 0.50 (151345 hom.)
• Consequence: PTPRA NM_001385305.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.22
• Publications: 5 publications found

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

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.76).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.782 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001385305.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PTPRA	NM_001385305.1	MANE Select	c.907-72T>A		intron	N/A	NP_001372234.1
	PTPRA	NM_001385302.1		c.940-72T>A		intron	N/A	NP_001372231.1
	PTPRA	NM_001385303.1		c.940-72T>A		intron	N/A	NP_001372232.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PTPRA	ENST00000399903.7	TSL:5 MANE Select	c.907-72T>A		intron	N/A	ENSP00000382787.2
	PTPRA	ENST00000216877.10	TSL:1	c.880-72T>A		intron	N/A	ENSP00000216877.6
	PTPRA	ENST00000356147.3	TSL:1	c.880-72T>A		intron	N/A	ENSP00000348468.3

Frequencies

GnomAD3 genomes AF: 0.530 AC: 80459 AN: 151896 Hom.: 21638 Cov.: 32

Gnomad AFR AF: 0.551

Gnomad AMI AF: 0.505

Gnomad AMR AF: 0.539

Gnomad ASJ AF: 0.425

Gnomad EAS AF: 0.802

Gnomad SAS AF: 0.618

Gnomad FIN AF: 0.522

Gnomad MID AF: 0.443

Gnomad NFE AF: 0.495

Gnomad OTH AF: 0.527

GnomAD4 exome AF: 0.504 AC: 586786 AN: 1163536 Hom.: 151345 AF XY: 0.507 AC XY: 300084 AN XY: 591358

African (AFR) AF: 0.543 AC: 14600 AN: 26912

American (AMR) AF: 0.533 AC: 21673 AN: 40634

Ashkenazi Jewish (ASJ) AF: 0.415 AC: 9902 AN: 23866

East Asian (EAS) AF: 0.851 AC: 32253 AN: 37920

South Asian (SAS) AF: 0.599 AC: 45867 AN: 76574

European-Finnish (FIN) AF: 0.528 AC: 23695 AN: 44852

Middle Eastern (MID) AF: 0.463 AC: 2408 AN: 5204

European-Non Finnish (NFE) AF: 0.480 AC: 411041 AN: 857082

Other (OTH) AF: 0.502 AC: 25347 AN: 50492

GnomAD4 genome AF: 0.530 AC: 80503 AN: 152014 Hom.: 21645 Cov.: 32 AF XY: 0.536 AC XY: 39834 AN XY: 74314

African (AFR) AF: 0.551 AC: 22809 AN: 41412

American (AMR) AF: 0.538 AC: 8233 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.425 AC: 1474 AN: 3470

East Asian (EAS) AF: 0.802 AC: 4156 AN: 5182

South Asian (SAS) AF: 0.617 AC: 2973 AN: 4818

European-Finnish (FIN) AF: 0.522 AC: 5507 AN: 10556

Middle Eastern (MID) AF: 0.452 AC: 133 AN: 294

European-Non Finnish (NFE) AF: 0.495 AC: 33646 AN: 67964

Other (OTH) AF: 0.528 AC: 1112 AN: 2108

Alfa AF: 0.505 Hom.: 2365

Bravo AF: 0.531

Asia WGS AF: 0.646 AC: 2247 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.76
CADD	Benign	11
DANN	Benign	0.79
PhyloP100		1.2
Mutation Taster		=99/1	polymorphism (auto)

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

Other links and lift over

dbSNP: rs1178015; hg19: chr20-2996423;