20-42365454-T-C

Variant names:

• chr20-42365454-T-C
• rs6030171
• NM_007050.6:c.1561-13169A>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.1561-13169A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.391 in 151,886 control chromosomes in the GnomAD database, including 12,067 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 0.39 (12067 hom., cov: 30)
• Consequence: PTPRT NM_007050.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.549
• Publications: 3 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=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.616 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.1561-13169A>G		intron	N/A	NP_008981.4
	PTPRT	NM_001394024.1		c.1561-13169A>G		intron	N/A	NP_001380953.1
	PTPRT	NM_133170.4		c.1561-13169A>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.1561-13169A>G		intron	N/A	ENSP00000362283.1	O14522-3
	PTPRT	ENST00000373193.7	TSL:1	c.1561-13169A>G		intron	N/A	ENSP00000362289.4	O14522-1
	PTPRT	ENST00000373198.8	TSL:1	c.1561-13169A>G		intron	N/A	ENSP00000362294.4	A0A075B6H0

Frequencies

GnomAD3 genomes AF: 0.390 AC: 59248 AN: 151768 Hom.: 12047 Cov.: 30

Gnomad AFR AF: 0.467

Gnomad AMI AF: 0.417

Gnomad AMR AF: 0.373

Gnomad ASJ AF: 0.328

Gnomad EAS AF: 0.635

Gnomad SAS AF: 0.380

Gnomad FIN AF: 0.335

Gnomad MID AF: 0.446

Gnomad NFE AF: 0.341

Gnomad OTH AF: 0.385

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

GnomAD4 genome AF: 0.391 AC: 59324 AN: 151886 Hom.: 12067 Cov.: 30 AF XY: 0.391 AC XY: 29028 AN XY: 74228

African (AFR) AF: 0.468 AC: 19341 AN: 41358

American (AMR) AF: 0.373 AC: 5702 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.328 AC: 1137 AN: 3462

East Asian (EAS) AF: 0.634 AC: 3270 AN: 5154

South Asian (SAS) AF: 0.380 AC: 1822 AN: 4796

European-Finnish (FIN) AF: 0.335 AC: 3535 AN: 10568

Middle Eastern (MID) AF: 0.442 AC: 129 AN: 292

European-Non Finnish (NFE) AF: 0.341 AC: 23183 AN: 67966

Other (OTH) AF: 0.392 AC: 825 AN: 2106

Alfa AF: 0.367 Hom.: 23769

Bravo AF: 0.402

Asia WGS AF: 0.551 AC: 1913 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.62
DANN	Benign	0.51
PhyloP100		-0.55
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: rs6030171; hg19: chr20-40994094;