rs6102794

Positions:

• chr20-42352362-C-A
• chr20-42352362-C-T

Variant summary

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

The NM_007050.6(PTPRT):​c.1561-77G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.273 in 1,468,512 control chromosomes in the GnomAD database, including 59,170 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 0.23 (4753 hom., cov: 32)
  • Exomes 𝑓: 0.28 (54417 hom.)
• Consequence: PTPRT NM_007050.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.61

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=-0.86).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.301 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PTPRT	NM_007050.6	c.1561-77G>T		intron_variant		ENST00000373187.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PTPRT	ENST00000373187.6	c.1561-77G>T		intron_variant		1	NM_007050.6	P4

Frequencies

GnomAD3 genomes AF: 0.226 AC: 34404 AN: 151980 Hom.: 4751 Cov.: 32

Gnomad AFR AF: 0.0849

Gnomad AMI AF: 0.180

Gnomad AMR AF: 0.268

Gnomad ASJ AF: 0.325

Gnomad EAS AF: 0.0367

Gnomad SAS AF: 0.100

Gnomad FIN AF: 0.336

Gnomad MID AF: 0.225

Gnomad NFE AF: 0.305

Gnomad OTH AF: 0.224

GnomAD4 exome AF: 0.278 AC: 366374 AN: 1316414 Hom.: 54417 AF XY: 0.273 AC XY: 180088 AN XY: 659400

Gnomad4 AFR exome AF: 0.0804

Gnomad4 AMR exome AF: 0.294

Gnomad4 ASJ exome AF: 0.323

Gnomad4 EAS exome AF: 0.0718

Gnomad4 SAS exome AF: 0.112

Gnomad4 FIN exome AF: 0.331

Gnomad4 NFE exome AF: 0.303

Gnomad4 OTH exome AF: 0.257

GnomAD4 genome AF: 0.226 AC: 34412 AN: 152098 Hom.: 4753 Cov.: 32 AF XY: 0.224 AC XY: 16662 AN XY: 74346

Gnomad4 AFR AF: 0.0851

Gnomad4 AMR AF: 0.268

Gnomad4 ASJ AF: 0.325

Gnomad4 EAS AF: 0.0366

Gnomad4 SAS AF: 0.100

Gnomad4 FIN AF: 0.336

Gnomad4 NFE AF: 0.305

Gnomad4 OTH AF: 0.221

Alfa AF: 0.287 Hom.: 8797

Bravo AF: 0.218

Asia WGS AF: 0.0910 AC: 317 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	0.30
DANN	Benign	0.34

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: rs6102794; hg19: chr20-40981002;