3-62188858-A-G

Variant names:

• chr3-62188858-A-G
• rs7641268
• NM_002841.4:c.1034-2611A>G

Variant summary

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

The NM_002841.4(PTPRG):​c.1034-2611A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.133 in 152,122 control chromosomes in the GnomAD database, including 1,536 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 0.13 (1536 hom., cov: 32)
• Consequence: PTPRG NM_002841.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.212
• Publications: 3 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=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.158 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_002841.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PTPRG	NM_002841.4	MANE Select	c.1034-2611A>G		intron	N/A	NP_002832.3
	PTPRG	NM_001375471.1		c.1034-2611A>G		intron	N/A	NP_001362400.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PTPRG	ENST00000474889.6	TSL:1 MANE Select	c.1034-2611A>G		intron	N/A	ENSP00000418112.1
	PTPRG	ENST00000295874.14	TSL:1	c.1034-2611A>G		intron	N/A	ENSP00000295874.10

Frequencies

GnomAD3 genomes AF: 0.133 AC: 20239 AN: 152004 Hom.: 1534 Cov.: 32

Gnomad AFR AF: 0.100

Gnomad AMI AF: 0.158

Gnomad AMR AF: 0.0867

Gnomad ASJ AF: 0.0709

Gnomad EAS AF: 0.0253

Gnomad SAS AF: 0.131

Gnomad FIN AF: 0.234

Gnomad MID AF: 0.0506

Gnomad NFE AF: 0.160

Gnomad OTH AF: 0.110

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

GnomAD4 genome AF: 0.133 AC: 20257 AN: 152122 Hom.: 1536 Cov.: 32 AF XY: 0.135 AC XY: 10051 AN XY: 74366

African (AFR) AF: 0.100 AC: 4159 AN: 41518

American (AMR) AF: 0.0865 AC: 1324 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.0709 AC: 246 AN: 3472

East Asian (EAS) AF: 0.0255 AC: 132 AN: 5174

South Asian (SAS) AF: 0.130 AC: 625 AN: 4806

European-Finnish (FIN) AF: 0.234 AC: 2473 AN: 10558

Middle Eastern (MID) AF: 0.0510 AC: 15 AN: 294

European-Non Finnish (NFE) AF: 0.160 AC: 10897 AN: 67976

Other (OTH) AF: 0.114 AC: 242 AN: 2116

Alfa AF: 0.141 Hom.: 3108

Bravo AF: 0.120

Asia WGS AF: 0.0950 AC: 329 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.2
DANN	Benign	0.50
PhyloP100		-0.21
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: rs7641268; hg19: chr3-62174532;