rs652889

Variant names:

• chr3-61808380-C-A
• rs652889
• NM_002841.4:c.190+59398C>A

Your query was ambiguous. Multiple possible variants found:

• chr3-61808380-C-A
• chr3-61808380-C-G
• chr3-61808380-C-T

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 17 publications found

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

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
PTPRG	NM_002841.4	c.190+59398C>A		intron_variant	Intron 2 of 29	ENST00000474889.6	NP_002832.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PTPRG	ENST00000474889.6	c.190+59398C>A		intron_variant	Intron 2 of 29	1	NM_002841.4	ENSP00000418112.1
PTPRG	ENST00000295874.14	c.190+59398C>A		intron_variant	Intron 2 of 28	1		ENSP00000295874.10

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

African (AFR) AF: 0.630 AC: 26103 AN: 41444

American (AMR) AF: 0.359 AC: 5476 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.337 AC: 1168 AN: 3464

East Asian (EAS) AF: 0.482 AC: 2472 AN: 5128

South Asian (SAS) AF: 0.511 AC: 2460 AN: 4816

European-Finnish (FIN) AF: 0.291 AC: 3061 AN: 10528

Middle Eastern (MID) AF: 0.456 AC: 134 AN: 294

European-Non Finnish (NFE) AF: 0.296 AC: 20109 AN: 67960

Other (OTH) AF: 0.402 AC: 850 AN: 2112

Alfa AF: 0.335 Hom.: 28502

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
PhyloP100		0.21
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs652889; hg19: chr3-61794054;