rs16988201

Variant names:

• chr20-3011439-C-T
• rs16988201
• NM_001385305.1:c.906+4019C>T

Variant summary

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

The NM_001385305.1(PTPRA):​c.906+4019C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0724 in 152,178 control chromosomes in the GnomAD database, including 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 0.072 (919 hom., cov: 32)
• Consequence: PTPRA NM_001385305.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.854
• Publications: 3 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=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.187 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PTPRA	NM_001385305.1	c.906+4019C>T		intron_variant	Intron 11 of 23	ENST00000399903.7	NP_001372234.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PTPRA	ENST00000399903.7	c.906+4019C>T		intron_variant	Intron 11 of 23	5	NM_001385305.1	ENSP00000382787.2
PTPRA	ENST00000216877.10	c.879+4019C>T		intron_variant	Intron 10 of 22	1		ENSP00000216877.6
PTPRA	ENST00000356147.3	c.879+4019C>T		intron_variant	Intron 10 of 22	1		ENSP00000348468.3
PTPRA	ENST00000318266.9	c.879+4019C>T		intron_variant	Intron 11 of 23	5		ENSP00000314568.5

Frequencies

GnomAD3 genomes AF: 0.0722 AC: 10976 AN: 152060 Hom.: 909 Cov.: 32

Gnomad AFR AF: 0.191

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.120

Gnomad ASJ AF: 0.0176

Gnomad EAS AF: 0.0814

Gnomad SAS AF: 0.0379

Gnomad FIN AF: 0.0160

Gnomad MID AF: 0.0443

Gnomad NFE AF: 0.00387

Gnomad OTH AF: 0.0660

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

GnomAD4 genome AF: 0.0724 AC: 11017 AN: 152178 Hom.: 919 Cov.: 32 AF XY: 0.0717 AC XY: 5337 AN XY: 74402

African (AFR) AF: 0.191 AC: 7919 AN: 41488

American (AMR) AF: 0.121 AC: 1849 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.0176 AC: 61 AN: 3468

East Asian (EAS) AF: 0.0814 AC: 421 AN: 5174

South Asian (SAS) AF: 0.0373 AC: 180 AN: 4824

European-Finnish (FIN) AF: 0.0160 AC: 170 AN: 10594

Middle Eastern (MID) AF: 0.0442 AC: 13 AN: 294

European-Non Finnish (NFE) AF: 0.00387 AC: 263 AN: 68016

Other (OTH) AF: 0.0667 AC: 141 AN: 2114

Alfa AF: 0.0322 Hom.: 149

Bravo AF: 0.0868

Asia WGS AF: 0.0930 AC: 323 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.13
DANN	Benign	0.37
PhyloP100		-0.85
Mutation Taster		=100/0	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: rs16988201; hg19: chr20-2992085;