rs652889

chr3-61808380-C-Achr3-61808380-C-Gchr3-61808380-C-T

Variant summary

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

The NM_002841.4(PTPRG):c.190+59398C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.408 in 151,926 control chromosomes in the GnomAD database, including 14,357 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 0.41 (14357 hom., cov: 31)
• Consequence: PTPRG NM_002841.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.209

Genes affected

PTPRG (HGNC:9671): (protein tyrosine phosphatase receptor type G) 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 possesses an extracellular region, a single transmembrane region, and two tandem intracytoplasmic catalytic domains, and thus represents a receptor-type PTP. The extracellular region of this PTP contains a carbonic anhydrase-like (CAH) domain, which is also found in the extracellular region of PTPRBETA/ZETA. This gene is located in a chromosomal region that is frequently deleted in renal cell carcinoma and lung carcinoma, thus is thought to be a candidate tumor suppressor gene. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.623 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PTPRG	NM_002841.4	c.190+59398C>A		intron_variant		ENST00000474889.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PTPRG	ENST00000474889.6	c.190+59398C>A		intron_variant		1	NM_002841.4	A1
PTPRG	ENST00000295874.14	c.190+59398C>A		intron_variant		1		P4

Frequencies

GnomAD3 genomes AF: 0.408 AC: 61892 AN: 151808 Hom.: 14315 Cov.: 31

Gnomad AFR AF: 0.629

Gnomad AMI AF: 0.177

Gnomad AMR AF: 0.359

Gnomad ASJ AF: 0.337

Gnomad EAS AF: 0.483

Gnomad SAS AF: 0.512

Gnomad FIN AF: 0.291

Gnomad MID AF: 0.440

Gnomad NFE AF: 0.296

Gnomad OTH AF: 0.400

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

GnomAD4 genome AF: 0.408 AC: 61994 AN: 151926 Hom.: 14357 Cov.: 31 AF XY: 0.410 AC XY: 30438 AN XY: 74238

Gnomad4 AFR AF: 0.630

Gnomad4 AMR AF: 0.359

Gnomad4 ASJ AF: 0.337

Gnomad4 EAS AF: 0.482

Gnomad4 SAS AF: 0.511

Gnomad4 FIN AF: 0.291

Gnomad4 NFE AF: 0.296

Gnomad4 OTH AF: 0.402

Alfa AF: 0.313 Hom.: 16576

Bravo AF: 0.418

Asia WGS AF: 0.538 AC: 1870 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	1.1
Dann	Benign	0.39

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.030		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: rs652889; hg19: chr3-61794054;