chr3-61617991-T-C

Position:

• chr3-61617991-T-C

Variant summary

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

The NM_002841.4(PTPRG):​c.85+55619T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.424 in 152,062 control chromosomes in the GnomAD database, including 15,212 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 0.42 (15212 hom., cov: 33)
• Consequence: PTPRG NM_002841.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0930

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

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.57).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.569 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
PTPRG	NM_002841.4	c.85+55619T>C		intron_variant		ENST00000474889.6	NP_002832.3
LOC124909388	XR_007095940.1	n.546+216T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
PTPRG	ENST00000474889.6	c.85+55619T>C		intron_variant		1	NM_002841.4	ENSP00000418112	A1
PTPRG	ENST00000295874.14	c.85+55619T>C		intron_variant		1		ENSP00000295874	P4
PTPRG	ENST00000495879.1	n.804+55619T>C		intron_variant, non_coding_transcript_variant		1
PTPRG	ENST00000475527.1	n.522+55619T>C		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.424 AC: 64401 AN: 151944 Hom.: 15214 Cov.: 33

Gnomad AFR AF: 0.193

Gnomad AMI AF: 0.465

Gnomad AMR AF: 0.468

Gnomad ASJ AF: 0.470

Gnomad EAS AF: 0.479

Gnomad SAS AF: 0.586

Gnomad FIN AF: 0.467

Gnomad MID AF: 0.601

Gnomad NFE AF: 0.527

Gnomad OTH AF: 0.459

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

GnomAD4 genome AF: 0.424 AC: 64404 AN: 152062 Hom.: 15212 Cov.: 33 AF XY: 0.428 AC XY: 31803 AN XY: 74338

Gnomad4 AFR AF: 0.192

Gnomad4 AMR AF: 0.468

Gnomad4 ASJ AF: 0.470

Gnomad4 EAS AF: 0.479

Gnomad4 SAS AF: 0.587

Gnomad4 FIN AF: 0.467

Gnomad4 NFE AF: 0.527

Gnomad4 OTH AF: 0.458

Alfa AF: 0.482 Hom.: 4571

Bravo AF: 0.409

Asia WGS AF: 0.501 AC: 1741 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.57
CADD	Benign	4.8
DANN	Benign	0.54

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		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: rs36051446; hg19: chr3-61603665;