chr20-42353702-G-A

Variant names:

• chr20-42353702-G-A
• rs6102795
• NM_007050.6:c.1561-1417C>T

Variant summary

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

The ENST00000373193.7(PTPRT):​c.1561-1417C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.298 in 152,068 control chromosomes in the GnomAD database, including 7,550 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 0.30 (7550 hom., cov: 32)
• Consequence: PTPRT ENST00000373193.7 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.694
• 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=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.776 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000373193.7. 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.1561-1417C>T		intron	N/A	NP_008981.4
	PTPRT	NM_001394024.1		c.1561-1417C>T		intron	N/A	NP_001380953.1
	PTPRT	NM_133170.4		c.1561-1417C>T		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.1561-1417C>T		intron	N/A	ENSP00000362283.1
	PTPRT	ENST00000373193.7	TSL:1	c.1561-1417C>T		intron	N/A	ENSP00000362289.4
	PTPRT	ENST00000373198.8	TSL:1	c.1561-1417C>T		intron	N/A	ENSP00000362294.4

Frequencies

GnomAD3 genomes AF: 0.298 AC: 45234 AN: 151950 Hom.: 7531 Cov.: 32

Gnomad AFR AF: 0.289

Gnomad AMI AF: 0.303

Gnomad AMR AF: 0.357

Gnomad ASJ AF: 0.213

Gnomad EAS AF: 0.796

Gnomad SAS AF: 0.391

Gnomad FIN AF: 0.265

Gnomad MID AF: 0.256

Gnomad NFE AF: 0.255

Gnomad OTH AF: 0.289

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

GnomAD4 genome AF: 0.298 AC: 45293 AN: 152068 Hom.: 7550 Cov.: 32 AF XY: 0.303 AC XY: 22536 AN XY: 74336

African (AFR) AF: 0.289 AC: 12003 AN: 41470

American (AMR) AF: 0.357 AC: 5464 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.213 AC: 738 AN: 3472

East Asian (EAS) AF: 0.796 AC: 4114 AN: 5166

South Asian (SAS) AF: 0.390 AC: 1878 AN: 4816

European-Finnish (FIN) AF: 0.265 AC: 2798 AN: 10562

Middle Eastern (MID) AF: 0.262 AC: 77 AN: 294

European-Non Finnish (NFE) AF: 0.255 AC: 17315 AN: 67976

Other (OTH) AF: 0.298 AC: 630 AN: 2116

Alfa AF: 0.272 Hom.: 13392

Bravo AF: 0.308

Asia WGS AF: 0.578 AC: 2007 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.38
DANN	Benign	0.52
PhyloP100		-0.69
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: rs6102795; hg19: chr20-40982342;