rs208194

chr20-42878246-G-Achr20-42878246-G-T

Variant summary

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

The NM_007050.6(PTPRT):c.214+7561C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.285 in 152,106 control chromosomes in the GnomAD database, including 6,404 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 0.29 (6404 hom., cov: 32)
• Consequence: PTPRT NM_007050.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.748

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=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.364 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PTPRT	NM_007050.6	c.214+7561C>T		intron_variant		ENST00000373187.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PTPRT	ENST00000373187.6	c.214+7561C>T		intron_variant		1	NM_007050.6	P4

Frequencies

GnomAD3 genomes AF: 0.285 AC: 43343 AN: 151988 Hom.: 6387 Cov.: 32

Gnomad AFR AF: 0.369

Gnomad AMI AF: 0.164

Gnomad AMR AF: 0.252

Gnomad ASJ AF: 0.219

Gnomad EAS AF: 0.202

Gnomad SAS AF: 0.262

Gnomad FIN AF: 0.273

Gnomad MID AF: 0.190

Gnomad NFE AF: 0.257

Gnomad OTH AF: 0.278

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

GnomAD4 genome AF: 0.285 AC: 43392 AN: 152106 Hom.: 6404 Cov.: 32 AF XY: 0.285 AC XY: 21160 AN XY: 74356

Gnomad4 AFR AF: 0.369

Gnomad4 AMR AF: 0.253

Gnomad4 ASJ AF: 0.219

Gnomad4 EAS AF: 0.202

Gnomad4 SAS AF: 0.261

Gnomad4 FIN AF: 0.273

Gnomad4 NFE AF: 0.257

Gnomad4 OTH AF: 0.274

Alfa AF: 0.261 Hom.: 4992

Bravo AF: 0.285

Asia WGS AF: 0.248 AC: 863 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	7.7
Dann	Benign	0.49

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: rs208194; hg19: chr20-41506886;