3-62007862-G-A

Variant names:

• chr3-62007862-G-A
• rs2107561
• NM_002841.4:c.519+4365G>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.519+4365G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.872 in 152,246 control chromosomes in the GnomAD database, including 58,048 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 0.87 (58048 hom., cov: 33)
• Consequence: PTPRG NM_002841.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0450
• Publications: 3 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=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.976 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PTPRG	NM_002841.4	c.519+4365G>A		intron_variant	Intron 4 of 29	ENST00000474889.6	NP_002832.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PTPRG	ENST00000474889.6	c.519+4365G>A		intron_variant	Intron 4 of 29	1	NM_002841.4	ENSP00000418112.1
PTPRG	ENST00000295874.14	c.519+4365G>A		intron_variant	Intron 4 of 28	1		ENSP00000295874.10

Frequencies

GnomAD3 genomes AF: 0.871 AC: 132555 AN: 152126 Hom.: 57980 Cov.: 33

Gnomad AFR AF: 0.917

Gnomad AMI AF: 0.588

Gnomad AMR AF: 0.898

Gnomad ASJ AF: 0.799

Gnomad EAS AF: 0.999

Gnomad SAS AF: 0.865

Gnomad FIN AF: 0.876

Gnomad MID AF: 0.787

Gnomad NFE AF: 0.835

Gnomad OTH AF: 0.865

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

GnomAD4 genome AF: 0.872 AC: 132687 AN: 152246 Hom.: 58048 Cov.: 33 AF XY: 0.874 AC XY: 65025 AN XY: 74414

African (AFR) AF: 0.917 AC: 38107 AN: 41548

American (AMR) AF: 0.899 AC: 13746 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.799 AC: 2772 AN: 3470

East Asian (EAS) AF: 0.999 AC: 5177 AN: 5182

South Asian (SAS) AF: 0.868 AC: 4189 AN: 4828

European-Finnish (FIN) AF: 0.876 AC: 9283 AN: 10596

Middle Eastern (MID) AF: 0.779 AC: 229 AN: 294

European-Non Finnish (NFE) AF: 0.835 AC: 56822 AN: 68012

Other (OTH) AF: 0.867 AC: 1827 AN: 2108

Alfa AF: 0.848 Hom.: 154794

Bravo AF: 0.876

Asia WGS AF: 0.934 AC: 3246 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	3.1
DANN	Benign	0.54
PhyloP100		-0.045
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: rs2107561; hg19: chr3-61993536;