rs7609954

chr3-61650482-G-T

Variant summary

Our verdict is Benign. Variant got -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

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

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PTPRG	NM_002841.4	c.85+88110G>T		intron_variant		ENST00000474889.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PTPRG	ENST00000474889.6	c.85+88110G>T		intron_variant		1	NM_002841.4	A1
PTPRG	ENST00000295874.14	c.85+88110G>T		intron_variant		1		P4
PTPRG	ENST00000495879.1	n.804+88110G>T		intron_variant, non_coding_transcript_variant		1
PTPRG	ENST00000475527.1	n.522+88110G>T		intron_variant, non_coding_transcript_variant		5

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

Gnomad4 AFR AF: 0.256

Gnomad4 AMR AF: 0.167

Gnomad4 ASJ AF: 0.0634

Gnomad4 EAS AF: 0.216

Gnomad4 SAS AF: 0.0742

Gnomad4 FIN AF: 0.153

Gnomad4 NFE AF: 0.127

Gnomad4 OTH AF: 0.144

Alfa AF: 0.145 Hom.: 417

Bravo AF: 0.173

Asia WGS AF: 0.150 AC: 522 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.26
Cadd	Benign	18
Dann	Benign	0.80

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

Publications

LitVar

Other links and lift over

dbSNP: rs7609954; hg19: chr3-61636156;