NM_002841.4:c.85+35237T>G

Variant names:

• chr3-61597609-T-G
• rs13074575
• NM_002841.4:c.85+35237T>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.85+35237T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0957 in 152,222 control chromosomes in the GnomAD database, including 770 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 0.096 (770 hom., cov: 32)
• Consequence: PTPRG NM_002841.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0710
• Publications: 6 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=-0.69).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.209 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.85+35237T>G		intron	N/A	NP_002832.3
	PTPRG	NM_001375471.1		c.85+35237T>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.85+35237T>G		intron	N/A	ENSP00000418112.1
	PTPRG	ENST00000295874.14	TSL:1	c.85+35237T>G		intron	N/A	ENSP00000295874.10
	PTPRG	ENST00000495879.1	TSL:1	n.804+35237T>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0957 AC: 14550 AN: 152104 Hom.: 772 Cov.: 32

Gnomad AFR AF: 0.0864

Gnomad AMI AF: 0.151

Gnomad AMR AF: 0.0951

Gnomad ASJ AF: 0.0547

Gnomad EAS AF: 0.220

Gnomad SAS AF: 0.0290

Gnomad FIN AF: 0.158

Gnomad MID AF: 0.0285

Gnomad NFE AF: 0.0892

Gnomad OTH AF: 0.0780

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

GnomAD4 genome AF: 0.0957 AC: 14564 AN: 152222 Hom.: 770 Cov.: 32 AF XY: 0.0981 AC XY: 7298 AN XY: 74424

African (AFR) AF: 0.0863 AC: 3588 AN: 41552

American (AMR) AF: 0.0947 AC: 1449 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.0547 AC: 190 AN: 3472

East Asian (EAS) AF: 0.220 AC: 1138 AN: 5176

South Asian (SAS) AF: 0.0299 AC: 144 AN: 4818

European-Finnish (FIN) AF: 0.158 AC: 1674 AN: 10586

Middle Eastern (MID) AF: 0.0306 AC: 9 AN: 294

European-Non Finnish (NFE) AF: 0.0892 AC: 6065 AN: 68008

Other (OTH) AF: 0.0805 AC: 170 AN: 2112

Alfa AF: 0.0940 Hom.: 101

Bravo AF: 0.0933

Asia WGS AF: 0.112 AC: 391 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.69
CADD	Benign	12
DANN	Benign	0.88
PhyloP100		0.071
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: rs13074575; hg19: chr3-61583283;