rs2206426

chr20-42657403-A-Gchr20-42657403-A-T

Variant summary

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

The NM_007050.6(PTPRT):c.1153+20463T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.49 in 152,000 control chromosomes in the GnomAD database, including 19,895 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 0.49 (19895 hom., cov: 31)
• Consequence: PTPRT NM_007050.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0390

Genes affected

PTPRT (HGNC:9682): (protein tyrosine phosphatase receptor type T) 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 intracellular catalytic domains, and thus represents a receptor-type PTP. The extracellular region contains a meprin-A5 antigen-PTP (MAM) domain, Ig-like and fibronectin type III-like repeats. The protein domain structure and the expression pattern of the mouse counterpart of this PTP suggest its roles in both signal transduction and cellular adhesion in the central nervous system. Two alternatively spliced transcript variants of this gene, which encode distinct proteins, have been reported. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.585 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PTPRT	NM_007050.6	c.1153+20463T>C		intron_variant		ENST00000373187.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PTPRT	ENST00000373187.6	c.1153+20463T>C		intron_variant		1	NM_007050.6	P4

Frequencies

GnomAD3 genomes AF: 0.491 AC: 74508 AN: 151884 Hom.: 19891 Cov.: 31

Gnomad AFR AF: 0.258

Gnomad AMI AF: 0.632

Gnomad AMR AF: 0.594

Gnomad ASJ AF: 0.633

Gnomad EAS AF: 0.589

Gnomad SAS AF: 0.568

Gnomad FIN AF: 0.575

Gnomad MID AF: 0.601

Gnomad NFE AF: 0.572

Gnomad OTH AF: 0.535

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

GnomAD4 genome AF: 0.490 AC: 74526 AN: 152000 Hom.: 19895 Cov.: 31 AF XY: 0.495 AC XY: 36760 AN XY: 74296

Gnomad4 AFR AF: 0.258

Gnomad4 AMR AF: 0.595

Gnomad4 ASJ AF: 0.633

Gnomad4 EAS AF: 0.588

Gnomad4 SAS AF: 0.568

Gnomad4 FIN AF: 0.575

Gnomad4 NFE AF: 0.572

Gnomad4 OTH AF: 0.534

Alfa AF: 0.565 Hom.: 49965

Bravo AF: 0.485

Asia WGS AF: 0.584 AC: 2031 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	1.1
Dann	Benign	0.63

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: rs2206426; hg19: chr20-41286043;