rs6513787

Variant names:

• chr20-42397266-C-A
• rs6513787
• NM_007050.6:c.1561-44981G>T

Variant summary

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

The NM_007050.6(PTPRT):​c.1561-44981G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.176 in 152,170 control chromosomes in the GnomAD database, including 5,271 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 0.18 (5271 hom., cov: 33)
• Consequence: PTPRT NM_007050.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.192
• 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=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.484 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.1561-44981G>T		intron	N/A	NP_008981.4
	PTPRT	NM_001394024.1		c.1561-44981G>T		intron	N/A	NP_001380953.1
	PTPRT	NM_133170.4		c.1561-44981G>T		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.1561-44981G>T		intron	N/A	ENSP00000362283.1	O14522-3
	PTPRT	ENST00000373193.7	TSL:1	c.1561-44981G>T		intron	N/A	ENSP00000362289.4	O14522-1
	PTPRT	ENST00000373198.8	TSL:1	c.1561-44981G>T		intron	N/A	ENSP00000362294.4	A0A075B6H0

Frequencies

GnomAD3 genomes AF: 0.176 AC: 26722 AN: 152052 Hom.: 5251 Cov.: 33

Gnomad AFR AF: 0.490

Gnomad AMI AF: 0.155

Gnomad AMR AF: 0.0832

Gnomad ASJ AF: 0.104

Gnomad EAS AF: 0.0183

Gnomad SAS AF: 0.0890

Gnomad FIN AF: 0.0347

Gnomad MID AF: 0.123

Gnomad NFE AF: 0.0512

Gnomad OTH AF: 0.136

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

GnomAD4 genome AF: 0.176 AC: 26780 AN: 152170 Hom.: 5271 Cov.: 33 AF XY: 0.170 AC XY: 12625 AN XY: 74406

African (AFR) AF: 0.490 AC: 20321 AN: 41476

American (AMR) AF: 0.0830 AC: 1270 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.104 AC: 360 AN: 3470

East Asian (EAS) AF: 0.0182 AC: 94 AN: 5174

South Asian (SAS) AF: 0.0884 AC: 427 AN: 4828

European-Finnish (FIN) AF: 0.0347 AC: 367 AN: 10590

Middle Eastern (MID) AF: 0.122 AC: 36 AN: 294

European-Non Finnish (NFE) AF: 0.0512 AC: 3480 AN: 68016

Other (OTH) AF: 0.134 AC: 284 AN: 2112

Alfa AF: 0.0911 Hom.: 3043

Bravo AF: 0.194

Asia WGS AF: 0.115 AC: 402 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	1.9
DANN	Benign	0.29
PhyloP100		0.19
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: rs6513787; hg19: chr20-41025906;