rs11917047

chr3-62120805-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_002841.4(PTPRG):c.616-11797G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.728 in 151,740 control chromosomes in the GnomAD database, including 40,472 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 0.73 (40472 hom., cov: 29)
• Consequence: PTPRG NM_002841.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.91

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 -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.04).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.755 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PTPRG	NM_002841.4	c.616-11797G>A		intron_variant		ENST00000474889.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PTPRG	ENST00000474889.6	c.616-11797G>A		intron_variant		1	NM_002841.4	A1
PTPRG	ENST00000295874.14	c.616-11797G>A		intron_variant		1		P4

Frequencies

GnomAD3 genomes AF: 0.728 AC: 110445 AN: 151622 Hom.: 40457 Cov.: 29

Gnomad AFR AF: 0.668

Gnomad AMI AF: 0.774

Gnomad AMR AF: 0.699

Gnomad ASJ AF: 0.754

Gnomad EAS AF: 0.743

Gnomad SAS AF: 0.684

Gnomad FIN AF: 0.799

Gnomad MID AF: 0.766

Gnomad NFE AF: 0.761

Gnomad OTH AF: 0.731

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

GnomAD4 genome AF: 0.728 AC: 110511 AN: 151740 Hom.: 40472 Cov.: 29 AF XY: 0.728 AC XY: 54000 AN XY: 74142

Gnomad4 AFR AF: 0.668

Gnomad4 AMR AF: 0.699

Gnomad4 ASJ AF: 0.754

Gnomad4 EAS AF: 0.743

Gnomad4 SAS AF: 0.684

Gnomad4 FIN AF: 0.799

Gnomad4 NFE AF: 0.761

Gnomad4 OTH AF: 0.731

Alfa AF: 0.738 Hom.: 7058

Bravo AF: 0.720

Asia WGS AF: 0.715 AC: 2490 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	0.079
Dann	Benign	0.43

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: rs11917047; hg19: chr3-62106479;