chr3-62049005-C-T

Variant names:

• chr3-62049005-C-T
• rs10490776
• NM_002841.4:c.520-29158C>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.520-29158C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0311 in 151,842 control chromosomes in the GnomAD database, including 106 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 0.031 (106 hom., cov: 33)
• Consequence: PTPRG NM_002841.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.974
• Publications: 2 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=-0.84).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.103 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PTPRG	NM_002841.4	c.520-29158C>T		intron_variant	Intron 4 of 29	ENST00000474889.6	NP_002832.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PTPRG	ENST00000474889.6	c.520-29158C>T		intron_variant	Intron 4 of 29	1	NM_002841.4	ENSP00000418112.1
PTPRG	ENST00000295874.14	c.520-29158C>T		intron_variant	Intron 4 of 28	1		ENSP00000295874.10

Frequencies

GnomAD3 genomes AF: 0.0311 AC: 4724 AN: 151726 Hom.: 107 Cov.: 33

Gnomad AFR AF: 0.0317

Gnomad AMI AF: 0.0330

Gnomad AMR AF: 0.0320

Gnomad ASJ AF: 0.00576

Gnomad EAS AF: 0.0345

Gnomad SAS AF: 0.111

Gnomad FIN AF: 0.00914

Gnomad MID AF: 0.0285

Gnomad NFE AF: 0.0292

Gnomad OTH AF: 0.0359

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

GnomAD4 genome AF: 0.0311 AC: 4720 AN: 151842 Hom.: 106 Cov.: 33 AF XY: 0.0319 AC XY: 2369 AN XY: 74192

African (AFR) AF: 0.0317 AC: 1311 AN: 41370

American (AMR) AF: 0.0319 AC: 486 AN: 15240

Ashkenazi Jewish (ASJ) AF: 0.00576 AC: 20 AN: 3470

East Asian (EAS) AF: 0.0344 AC: 178 AN: 5170

South Asian (SAS) AF: 0.111 AC: 535 AN: 4808

European-Finnish (FIN) AF: 0.00914 AC: 96 AN: 10500

Middle Eastern (MID) AF: 0.0272 AC: 8 AN: 294

European-Non Finnish (NFE) AF: 0.0292 AC: 1984 AN: 67966

Other (OTH) AF: 0.0341 AC: 72 AN: 2114

Alfa AF: 0.0262 Hom.: 84

Bravo AF: 0.0315

Asia WGS AF: 0.0680 AC: 238 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	11
DANN	Benign	0.52
PhyloP100		0.97
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: rs10490776; hg19: chr3-62034679;