rs7632091

Variant names:

• chr3-62149128-T-C
• rs7632091
• NM_002841.4:c.683-7939T>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.683-7939T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.272 in 152,106 control chromosomes in the GnomAD database, including 6,728 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 0.27 (6728 hom., cov: 32)
• Consequence: PTPRG NM_002841.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.91
• Publications: 1 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]

ENSG00000297925 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.453 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PTPRG	NM_002841.4	c.683-7939T>C		intron_variant	Intron 6 of 29	ENST00000474889.6	NP_002832.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PTPRG	ENST00000474889.6	c.683-7939T>C		intron_variant	Intron 6 of 29	1	NM_002841.4	ENSP00000418112.1
PTPRG	ENST00000295874.14	c.683-7939T>C		intron_variant	Intron 6 of 28	1		ENSP00000295874.10
ENSG00000297925	ENST00000751855.1	n.218+718A>G		intron_variant	Intron 1 of 1
ENSG00000297925	ENST00000751856.1	n.218+718A>G		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.272 AC: 41282 AN: 151988 Hom.: 6714 Cov.: 32

Gnomad AFR AF: 0.458

Gnomad AMI AF: 0.226

Gnomad AMR AF: 0.159

Gnomad ASJ AF: 0.261

Gnomad EAS AF: 0.0179

Gnomad SAS AF: 0.192

Gnomad FIN AF: 0.295

Gnomad MID AF: 0.208

Gnomad NFE AF: 0.207

Gnomad OTH AF: 0.258

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

GnomAD4 genome AF: 0.272 AC: 41349 AN: 152106 Hom.: 6728 Cov.: 32 AF XY: 0.272 AC XY: 20191 AN XY: 74358

African (AFR) AF: 0.458 AC: 18991 AN: 41454

American (AMR) AF: 0.159 AC: 2429 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.261 AC: 905 AN: 3472

East Asian (EAS) AF: 0.0180 AC: 93 AN: 5180

South Asian (SAS) AF: 0.192 AC: 923 AN: 4810

European-Finnish (FIN) AF: 0.295 AC: 3124 AN: 10576

Middle Eastern (MID) AF: 0.224 AC: 65 AN: 290

European-Non Finnish (NFE) AF: 0.207 AC: 14060 AN: 68000

Other (OTH) AF: 0.262 AC: 553 AN: 2112

Alfa AF: 0.227 Hom.: 13263

Bravo AF: 0.271

Asia WGS AF: 0.144 AC: 501 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.18
DANN	Benign	0.37
PhyloP100		-1.9
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: rs7632091; hg19: chr3-62134802;