rs7609954

Variant names:

• chr3-61650482-G-T
• rs7609954
• NM_002841.4:c.85+88110G>T

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The NM_002841.4(PTPRG):​c.85+88110G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.168 in 152,118 control chromosomes in the GnomAD database, including 2,445 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 0.17 (2445 hom., cov: 32)
• Consequence: PTPRG NM_002841.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.31
• Publications: 13 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]

ENSG00000298427 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.26).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.252 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+88110G>T		intron	N/A	NP_002832.3
	PTPRG	NM_001375471.1		c.85+88110G>T		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+88110G>T		intron	N/A	ENSP00000418112.1
	PTPRG	ENST00000295874.14	TSL:1	c.85+88110G>T		intron	N/A	ENSP00000295874.10
	PTPRG	ENST00000495879.1	TSL:1	n.804+88110G>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.168 AC: 25552 AN: 152000 Hom.: 2434 Cov.: 32

Gnomad AFR AF: 0.255

Gnomad AMI AF: 0.122

Gnomad AMR AF: 0.168

Gnomad ASJ AF: 0.0634

Gnomad EAS AF: 0.216

Gnomad SAS AF: 0.0731

Gnomad FIN AF: 0.153

Gnomad MID AF: 0.146

Gnomad NFE AF: 0.127

Gnomad OTH AF: 0.143

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

GnomAD4 genome AF: 0.168 AC: 25607 AN: 152118 Hom.: 2445 Cov.: 32 AF XY: 0.168 AC XY: 12527 AN XY: 74356

African (AFR) AF: 0.256 AC: 10603 AN: 41476

American (AMR) AF: 0.167 AC: 2557 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.0634 AC: 220 AN: 3472

East Asian (EAS) AF: 0.216 AC: 1116 AN: 5160

South Asian (SAS) AF: 0.0742 AC: 358 AN: 4824

European-Finnish (FIN) AF: 0.153 AC: 1624 AN: 10584

Middle Eastern (MID) AF: 0.153 AC: 45 AN: 294

European-Non Finnish (NFE) AF: 0.127 AC: 8669 AN: 68004

Other (OTH) AF: 0.144 AC: 304 AN: 2112

Alfa AF: 0.143 Hom.: 625

Bravo AF: 0.173

Asia WGS AF: 0.150 AC: 522 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.26
CADD	Benign	18
DANN	Benign	0.80
PhyloP100		2.3
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: rs7609954; hg19: chr3-61636156;