rs11917047

Variant names:

• chr3-62120805-G-A
• rs11917047
• NM_002841.4:c.616-11797G>A

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 2 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]

ENSG00000302838 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
PTPRG	NM_002841.4	c.616-11797G>A		intron_variant	Intron 5 of 29	ENST00000474889.6	NP_002832.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PTPRG	ENST00000474889.6	c.616-11797G>A		intron_variant	Intron 5 of 29	1	NM_002841.4	ENSP00000418112.1
PTPRG	ENST00000295874.14	c.616-11797G>A		intron_variant	Intron 5 of 28	1		ENSP00000295874.10
ENSG00000302838	ENST00000789916.1	n.57-7824C>T		intron_variant	Intron 1 of 3

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

African (AFR) AF: 0.668 AC: 27588 AN: 41322

American (AMR) AF: 0.699 AC: 10674 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.754 AC: 2616 AN: 3470

East Asian (EAS) AF: 0.743 AC: 3821 AN: 5142

South Asian (SAS) AF: 0.684 AC: 3285 AN: 4804

European-Finnish (FIN) AF: 0.799 AC: 8396 AN: 10502

Middle Eastern (MID) AF: 0.752 AC: 221 AN: 294

European-Non Finnish (NFE) AF: 0.761 AC: 51663 AN: 67922

Other (OTH) AF: 0.731 AC: 1543 AN: 2110

Alfa AF: 0.737 Hom.: 7230

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
PhyloP100		-2.9
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: rs11917047; hg19: chr3-62106479;