20-42574295-T-C

Variant names:

• chr20-42574295-T-C
• rs6102912
• NM_007050.6:c.1154-101733A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_007050.6(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 NM_007050.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.346
• Publications: 5 publications found

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

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_007050.6. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PTPRT	NM_007050.6	MANE Select	c.1154-101733A>G		intron	N/A	NP_008981.4
	PTPRT	NM_001394024.1		c.1154-101733A>G		intron	N/A	NP_001380953.1
	PTPRT	NM_133170.4		c.1154-101733A>G		intron	N/A	NP_573400.3

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PTPRT	ENST00000373187.6	TSL:1 MANE Select	c.1154-101733A>G		intron	N/A	ENSP00000362283.1
	PTPRT	ENST00000373193.7	TSL:1	c.1154-101733A>G		intron	N/A	ENSP00000362289.4
	PTPRT	ENST00000373198.8	TSL:1	c.1154-101733A>G		intron	N/A	ENSP00000362294.4

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

African (AFR) AF: 0.523 AC: 21659 AN: 41410

American (AMR) AF: 0.531 AC: 8104 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.590 AC: 2044 AN: 3466

East Asian (EAS) AF: 0.628 AC: 3241 AN: 5158

South Asian (SAS) AF: 0.522 AC: 2511 AN: 4810

European-Finnish (FIN) AF: 0.516 AC: 5444 AN: 10542

Middle Eastern (MID) AF: 0.401 AC: 117 AN: 292

European-Non Finnish (NFE) AF: 0.424 AC: 28779 AN: 67918

Other (OTH) AF: 0.463 AC: 974 AN: 2102

Alfa AF: 0.449 Hom.: 10152

Bravo AF: 0.487

Asia WGS AF: 0.574 AC: 1997 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.73
CADD	Benign	13
DANN	Benign	0.49
PhyloP100		0.35
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs6102912; hg19: chr20-41202935;