20-42574295-T-C

Position:

• chr20-42574295-T-C

Variant summary

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

The ENST00000373187.6(PTPRT):​c.1154-101733A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.482 in 151,872 control chromosomes in the GnomAD database, including 17,890 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 0.48 (17890 hom., cov: 32)
• Consequence: PTPRT ENST00000373187.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.346

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=-0.73).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.61 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
PTPRT	NM_007050.6	c.1154-101733A>G		intron_variant		ENST00000373187.6	NP_008981.4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
PTPRT	ENST00000373187.6	c.1154-101733A>G		intron_variant		1	NM_007050.6	ENSP00000362283	P4

Frequencies

GnomAD3 genomes AF: 0.482 AC: 73134 AN: 151756 Hom.: 17881 Cov.: 32

Gnomad AFR AF: 0.524

Gnomad AMI AF: 0.331

Gnomad AMR AF: 0.531

Gnomad ASJ AF: 0.590

Gnomad EAS AF: 0.627

Gnomad SAS AF: 0.523

Gnomad FIN AF: 0.516

Gnomad MID AF: 0.399

Gnomad NFE AF: 0.424

Gnomad OTH AF: 0.464

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

GnomAD4 genome AF: 0.482 AC: 73175 AN: 151872 Hom.: 17890 Cov.: 32 AF XY: 0.489 AC XY: 36267 AN XY: 74200

Gnomad4 AFR AF: 0.523

Gnomad4 AMR AF: 0.531

Gnomad4 ASJ AF: 0.590

Gnomad4 EAS AF: 0.628

Gnomad4 SAS AF: 0.522

Gnomad4 FIN AF: 0.516

Gnomad4 NFE AF: 0.424

Gnomad4 OTH AF: 0.463

Alfa AF: 0.449 Hom.: 7670

Bravo AF: 0.487

Asia WGS AF: 0.574 AC: 1997 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.73
CADD	Benign	13
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: rs6102912; hg19: chr20-41202935;