rs13074575

chr3-61597609-T-G

Variant summary

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

The NM_002841.4(PTPRG):c.85+35237T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0957 in 152,222 control chromosomes in the GnomAD database, including 770 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 0.096 (770 hom., cov: 32)
• Consequence: PTPRG NM_002841.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0710

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=-0.69).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.209 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PTPRG	NM_002841.4	c.85+35237T>G		intron_variant		ENST00000474889.6
PTPRG	NM_001375471.1	c.85+35237T>G		intron_variant
PTPRG	XM_017006961.2	c.85+35237T>G		intron_variant
PTPRG	XM_017006963.2	c.85+35237T>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PTPRG	ENST00000474889.6	c.85+35237T>G		intron_variant		1	NM_002841.4	A1
PTPRG	ENST00000295874.14	c.85+35237T>G		intron_variant		1		P4
PTPRG	ENST00000495879.1	n.804+35237T>G		intron_variant, non_coding_transcript_variant		1
PTPRG	ENST00000475527.1	n.522+35237T>G		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.0957 AC: 14550 AN: 152104 Hom.: 772 Cov.: 32

Gnomad AFR AF: 0.0864

Gnomad AMI AF: 0.151

Gnomad AMR AF: 0.0951

Gnomad ASJ AF: 0.0547

Gnomad EAS AF: 0.220

Gnomad SAS AF: 0.0290

Gnomad FIN AF: 0.158

Gnomad MID AF: 0.0285

Gnomad NFE AF: 0.0892

Gnomad OTH AF: 0.0780

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

GnomAD4 genome AF: 0.0957 AC: 14564 AN: 152222 Hom.: 770 Cov.: 32 AF XY: 0.0981 AC XY: 7298 AN XY: 74424

Gnomad4 AFR AF: 0.0863

Gnomad4 AMR AF: 0.0947

Gnomad4 ASJ AF: 0.0547

Gnomad4 EAS AF: 0.220

Gnomad4 SAS AF: 0.0299

Gnomad4 FIN AF: 0.158

Gnomad4 NFE AF: 0.0892

Gnomad4 OTH AF: 0.0805

Alfa AF: 0.0940 Hom.: 99

Bravo AF: 0.0933

Asia WGS AF: 0.112 AC: 391 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.69
Cadd	Benign	12
Dann	Benign	0.88

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: rs13074575; hg19: chr3-61583283;