rs2782641

Positions:

• chr1-43547684-G-A
• chr1-43547684-G-C

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The NM_002840.5(PTPRF):​c.91+2518G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.657 in 152,194 control chromosomes in the GnomAD database, including 33,106 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 0.66 (33106 hom., cov: 33)
• Consequence: PTPRF NM_002840.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.657

Genes affected

PTPRF (HGNC:9670): (protein tyrosine phosphatase receptor type F) 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 contains three Ig-like domains, and nine non-Ig like domains similar to that of neural-cell adhesion molecule. This PTP was shown to function in the regulation of epithelial cell-cell contacts at adherents junctions, as well as in the control of beta-catenin signaling. An increased expression level of this protein was found in the insulin-responsive tissue of obese, insulin-resistant individuals, and may contribute to the pathogenesis of insulin resistance. Two alternatively spliced transcript variants of this gene, which encode distinct proteins, have been reported. [provided by RefSeq, Jul 2008]

PTPRF (HGNC:):

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.28).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.812 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
PTPRF	NM_002840.5	c.91+2518G>A		intron_variant		ENST00000359947.9	NP_002831.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
PTPRF	ENST00000359947.9	c.91+2518G>A		intron_variant		1	NM_002840.5	ENSP00000353030.4

Frequencies

GnomAD3 genomes AF: 0.657 AC: 99943 AN: 152076 Hom.: 33089 Cov.: 33

Gnomad AFR AF: 0.686

Gnomad AMI AF: 0.601

Gnomad AMR AF: 0.687

Gnomad ASJ AF: 0.651

Gnomad EAS AF: 0.767

Gnomad SAS AF: 0.835

Gnomad FIN AF: 0.621

Gnomad MID AF: 0.611

Gnomad NFE AF: 0.620

Gnomad OTH AF: 0.631

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

GnomAD4 genome AF: 0.657 AC: 100008 AN: 152194 Hom.: 33106 Cov.: 33 AF XY: 0.661 AC XY: 49204 AN XY: 74412

Gnomad4 AFR AF: 0.686

Gnomad4 AMR AF: 0.687

Gnomad4 ASJ AF: 0.651

Gnomad4 EAS AF: 0.767

Gnomad4 SAS AF: 0.833

Gnomad4 FIN AF: 0.621

Gnomad4 NFE AF: 0.620

Gnomad4 OTH AF: 0.631

Alfa AF: 0.628 Hom.: 30347

Bravo AF: 0.661

Asia WGS AF: 0.801 AC: 2786 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.28
CADD	Benign	16
DANN	Benign	0.84

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: rs2782641; hg19: chr1-44013355;