rs6072690

Variant names:

• chr20-42343061-G-A
• rs6072690
• NM_007050.6:c.1865+7567C>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.1865+7567C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.449 in 151,844 control chromosomes in the GnomAD database, including 15,518 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 0.45 (15518 hom., cov: 31)
• Consequence: PTPRT NM_007050.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.26
• Publications: 1 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=-0.81).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.508 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PTPRT	NM_007050.6	c.1865+7567C>T		intron_variant	Intron 11 of 30	ENST00000373187.6	NP_008981.4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PTPRT	ENST00000373187.6	c.1865+7567C>T		intron_variant	Intron 11 of 30	1	NM_007050.6	ENSP00000362283.1
PTPRT	ENST00000373193.7	c.1865+7567C>T		intron_variant	Intron 11 of 31	1		ENSP00000362289.4
PTPRT	ENST00000617474.1	n.*1723+7567C>T		intron_variant	Intron 11 of 30	5		ENSP00000484248.1

Frequencies

GnomAD3 genomes AF: 0.449 AC: 68101 AN: 151726 Hom.: 15498 Cov.: 31

Gnomad AFR AF: 0.514

Gnomad AMI AF: 0.626

Gnomad AMR AF: 0.471

Gnomad ASJ AF: 0.429

Gnomad EAS AF: 0.354

Gnomad SAS AF: 0.495

Gnomad FIN AF: 0.373

Gnomad MID AF: 0.446

Gnomad NFE AF: 0.419

Gnomad OTH AF: 0.449

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

GnomAD4 genome AF: 0.449 AC: 68167 AN: 151844 Hom.: 15518 Cov.: 31 AF XY: 0.448 AC XY: 33232 AN XY: 74222

African (AFR) AF: 0.514 AC: 21268 AN: 41378

American (AMR) AF: 0.471 AC: 7200 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.429 AC: 1490 AN: 3470

East Asian (EAS) AF: 0.354 AC: 1817 AN: 5140

South Asian (SAS) AF: 0.497 AC: 2390 AN: 4812

European-Finnish (FIN) AF: 0.373 AC: 3930 AN: 10534

Middle Eastern (MID) AF: 0.456 AC: 134 AN: 294

European-Non Finnish (NFE) AF: 0.418 AC: 28424 AN: 67920

Other (OTH) AF: 0.447 AC: 944 AN: 2110

Alfa AF: 0.428 Hom.: 19832

Bravo AF: 0.455

Asia WGS AF: 0.485 AC: 1689 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	5.0
DANN	Benign	0.62
PhyloP100		1.3
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: rs6072690; hg19: chr20-40971701;