3-61634792-T-C

Variant names:

• chr3-61634792-T-C
• rs17624623
• NM_002841.4:c.85+72420T>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_002841.4(PTPRG):​c.85+72420T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.36 in 151,942 control chromosomes in the GnomAD database, including 10,314 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 0.36 (10314 hom., cov: 31)
• Consequence: PTPRG NM_002841.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.651
• 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]

LOC124909388 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.75).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.411 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PTPRG	NM_002841.4	c.85+72420T>C		intron_variant	Intron 1 of 29	ENST00000474889.6	NP_002832.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PTPRG	ENST00000474889.6	c.85+72420T>C		intron_variant	Intron 1 of 29	1	NM_002841.4	ENSP00000418112.1
PTPRG	ENST00000295874.14	c.85+72420T>C		intron_variant	Intron 1 of 28	1		ENSP00000295874.10
PTPRG	ENST00000495879.1	n.804+72420T>C		intron_variant	Intron 1 of 2	1
PTPRG	ENST00000475527.1	n.522+72420T>C		intron_variant	Intron 1 of 1	5

Frequencies

GnomAD3 genomes AF: 0.360 AC: 54714 AN: 151826 Hom.: 10315 Cov.: 31

Gnomad AFR AF: 0.256

Gnomad AMI AF: 0.495

Gnomad AMR AF: 0.363

Gnomad ASJ AF: 0.497

Gnomad EAS AF: 0.252

Gnomad SAS AF: 0.379

Gnomad FIN AF: 0.398

Gnomad MID AF: 0.440

Gnomad NFE AF: 0.415

Gnomad OTH AF: 0.387

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

GnomAD4 genome AF: 0.360 AC: 54742 AN: 151942 Hom.: 10314 Cov.: 31 AF XY: 0.357 AC XY: 26511 AN XY: 74240

African (AFR) AF: 0.256 AC: 10599 AN: 41460

American (AMR) AF: 0.363 AC: 5541 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.497 AC: 1725 AN: 3468

East Asian (EAS) AF: 0.252 AC: 1299 AN: 5152

South Asian (SAS) AF: 0.378 AC: 1825 AN: 4822

European-Finnish (FIN) AF: 0.398 AC: 4189 AN: 10538

Middle Eastern (MID) AF: 0.439 AC: 129 AN: 294

European-Non Finnish (NFE) AF: 0.415 AC: 28168 AN: 67936

Other (OTH) AF: 0.389 AC: 817 AN: 2098

Alfa AF: 0.402 Hom.: 52631

Bravo AF: 0.353

Asia WGS AF: 0.338 AC: 1177 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.75
CADD	Benign	7.4
DANN	Benign	0.86
PhyloP100		0.65
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: rs17624623; hg19: chr3-61620466;