rs6072694

Variant names:

• chr20-42353465-C-T
• rs6072694
• NM_007050.6:c.1561-1180G>A

Variant summary

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

The NM_133170.4(PTPRT):​c.1561-1180G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.182 in 151,986 control chromosomes in the GnomAD database, including 3,075 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 (3075 hom., cov: 32)
• Consequence: PTPRT NM_133170.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.353
• Publications: 4 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=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.303 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_133170.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PTPRT	NM_007050.6	MANE Select	c.1561-1180G>A		intron	N/A	NP_008981.4
	PTPRT	NM_001394024.1		c.1561-1180G>A		intron	N/A	NP_001380953.1
	PTPRT	NM_133170.4		c.1561-1180G>A		intron	N/A	NP_573400.3

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PTPRT	ENST00000373187.6	TSL:1 MANE Select	c.1561-1180G>A		intron	N/A	ENSP00000362283.1
	PTPRT	ENST00000373193.7	TSL:1	c.1561-1180G>A		intron	N/A	ENSP00000362289.4
	PTPRT	ENST00000373198.8	TSL:1	c.1561-1180G>A		intron	N/A	ENSP00000362294.4

Frequencies

GnomAD3 genomes AF: 0.182 AC: 27583 AN: 151868 Hom.: 3061 Cov.: 32

Gnomad AFR AF: 0.308

Gnomad AMI AF: 0.135

Gnomad AMR AF: 0.122

Gnomad ASJ AF: 0.108

Gnomad EAS AF: 0.0338

Gnomad SAS AF: 0.219

Gnomad FIN AF: 0.119

Gnomad MID AF: 0.149

Gnomad NFE AF: 0.142

Gnomad OTH AF: 0.177

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

GnomAD4 genome AF: 0.182 AC: 27629 AN: 151986 Hom.: 3075 Cov.: 32 AF XY: 0.179 AC XY: 13330 AN XY: 74296

African (AFR) AF: 0.308 AC: 12743 AN: 41396

American (AMR) AF: 0.122 AC: 1863 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.108 AC: 376 AN: 3468

East Asian (EAS) AF: 0.0338 AC: 175 AN: 5172

South Asian (SAS) AF: 0.220 AC: 1058 AN: 4810

European-Finnish (FIN) AF: 0.119 AC: 1254 AN: 10566

Middle Eastern (MID) AF: 0.163 AC: 48 AN: 294

European-Non Finnish (NFE) AF: 0.142 AC: 9621 AN: 67984

Other (OTH) AF: 0.175 AC: 368 AN: 2108

Alfa AF: 0.154 Hom.: 8749

Bravo AF: 0.184

Asia WGS AF: 0.122 AC: 424 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	2.8
DANN	Benign	0.37
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: rs6072694; hg19: chr20-40982105;