rs704343

Positions:

• chr3-62000054-A-G

Variant summary

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

The NM_002841.4(PTPRG):​c.371-3295A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.536 in 151,938 control chromosomes in the GnomAD database, including 22,442 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 0.54 (22442 hom., cov: 31)
• Consequence: PTPRG NM_002841.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.03

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=-1.04).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.658 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
PTPRG	NM_002841.4	c.371-3295A>G		intron_variant		ENST00000474889.6	NP_002832.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
PTPRG	ENST00000474889.6	c.371-3295A>G		intron_variant		1	NM_002841.4	ENSP00000418112	A1
PTPRG	ENST00000295874.14	c.371-3295A>G		intron_variant		1		ENSP00000295874	P4

Frequencies

GnomAD3 genomes AF: 0.536 AC: 81321 AN: 151820 Hom.: 22425 Cov.: 31

Gnomad AFR AF: 0.665

Gnomad AMI AF: 0.453

Gnomad AMR AF: 0.428

Gnomad ASJ AF: 0.583

Gnomad EAS AF: 0.380

Gnomad SAS AF: 0.477

Gnomad FIN AF: 0.450

Gnomad MID AF: 0.541

Gnomad NFE AF: 0.509

Gnomad OTH AF: 0.524

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

GnomAD4 genome AF: 0.536 AC: 81371 AN: 151938 Hom.: 22442 Cov.: 31 AF XY: 0.529 AC XY: 39299 AN XY: 74222

Gnomad4 AFR AF: 0.665

Gnomad4 AMR AF: 0.428

Gnomad4 ASJ AF: 0.583

Gnomad4 EAS AF: 0.381

Gnomad4 SAS AF: 0.476

Gnomad4 FIN AF: 0.450

Gnomad4 NFE AF: 0.509

Gnomad4 OTH AF: 0.520

Alfa AF: 0.531 Hom.: 2633

Bravo AF: 0.538

Asia WGS AF: 0.455 AC: 1583 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.81
DANN	Benign	0.69

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: rs704343; hg19: chr3-61985728;