3-62057151-T-C

Variant names:

• chr3-62057151-T-C
• rs17065828
• NM_002841.4:c.520-21012T>C

Variant summary

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

The NM_002841.4(PTPRG):​c.520-21012T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.21 in 152,070 control chromosomes in the GnomAD database, including 3,502 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 0.21 (3502 hom., cov: 32)
• Consequence: PTPRG NM_002841.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.819
• Publications: 4 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]

ENSG00000294605 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.72).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.265 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PTPRG	NM_002841.4	c.520-21012T>C		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.520-21012T>C		intron_variant	Intron 4 of 29	1	NM_002841.4	ENSP00000418112.1
PTPRG	ENST00000295874.14	c.520-21012T>C		intron_variant	Intron 4 of 28	1		ENSP00000295874.10
ENSG00000294605	ENST00000724690.1	n.205+161A>G		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.210 AC: 31955 AN: 151952 Hom.: 3498 Cov.: 32

Gnomad AFR AF: 0.203

Gnomad AMI AF: 0.318

Gnomad AMR AF: 0.271

Gnomad ASJ AF: 0.265

Gnomad EAS AF: 0.245

Gnomad SAS AF: 0.170

Gnomad FIN AF: 0.124

Gnomad MID AF: 0.171

Gnomad NFE AF: 0.210

Gnomad OTH AF: 0.224

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

GnomAD4 genome AF: 0.210 AC: 31991 AN: 152070 Hom.: 3502 Cov.: 32 AF XY: 0.206 AC XY: 15333 AN XY: 74348

African (AFR) AF: 0.203 AC: 8412 AN: 41464

American (AMR) AF: 0.272 AC: 4154 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.265 AC: 919 AN: 3468

East Asian (EAS) AF: 0.244 AC: 1263 AN: 5168

South Asian (SAS) AF: 0.170 AC: 820 AN: 4816

European-Finnish (FIN) AF: 0.124 AC: 1308 AN: 10584

Middle Eastern (MID) AF: 0.177 AC: 52 AN: 294

European-Non Finnish (NFE) AF: 0.210 AC: 14296 AN: 67982

Other (OTH) AF: 0.226 AC: 478 AN: 2116

Alfa AF: 0.217 Hom.: 15530

Bravo AF: 0.225

Asia WGS AF: 0.219 AC: 761 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.72
CADD	Benign	14
DANN	Benign	0.87
PhyloP100		0.82
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: rs17065828; hg19: chr3-62042825;