chr20-42807024-T-C

Variant names:

• chr20-42807024-T-C
• rs490514
• NM_007050.6:c.215-15558A>G

Variant summary

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

The ENST00000373193.7(PTPRT):​c.215-15558A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.142 in 152,090 control chromosomes in the GnomAD database, including 1,767 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 0.14 (1767 hom., cov: 32)
• Consequence: PTPRT ENST00000373193.7 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.672
• 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=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.369 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.215-15558A>G		intron	N/A	NP_008981.4
	PTPRT	NM_001394024.1		c.215-15558A>G		intron	N/A	NP_001380953.1
	PTPRT	NM_133170.4		c.215-15558A>G		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.215-15558A>G		intron	N/A	ENSP00000362283.1
	PTPRT	ENST00000373193.7	TSL:1	c.215-15558A>G		intron	N/A	ENSP00000362289.4
	PTPRT	ENST00000373198.8	TSL:1	c.215-15558A>G		intron	N/A	ENSP00000362294.4

Frequencies

GnomAD3 genomes AF: 0.142 AC: 21612 AN: 151974 Hom.: 1761 Cov.: 32

Gnomad AFR AF: 0.128

Gnomad AMI AF: 0.233

Gnomad AMR AF: 0.165

Gnomad ASJ AF: 0.134

Gnomad EAS AF: 0.383

Gnomad SAS AF: 0.207

Gnomad FIN AF: 0.117

Gnomad MID AF: 0.206

Gnomad NFE AF: 0.126

Gnomad OTH AF: 0.149

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

GnomAD4 genome AF: 0.142 AC: 21636 AN: 152090 Hom.: 1767 Cov.: 32 AF XY: 0.145 AC XY: 10752 AN XY: 74340

African (AFR) AF: 0.128 AC: 5307 AN: 41508

American (AMR) AF: 0.165 AC: 2514 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.134 AC: 465 AN: 3470

East Asian (EAS) AF: 0.383 AC: 1964 AN: 5132

South Asian (SAS) AF: 0.206 AC: 992 AN: 4808

European-Finnish (FIN) AF: 0.117 AC: 1238 AN: 10598

Middle Eastern (MID) AF: 0.221 AC: 65 AN: 294

European-Non Finnish (NFE) AF: 0.126 AC: 8556 AN: 67980

Other (OTH) AF: 0.153 AC: 323 AN: 2114

Alfa AF: 0.132 Hom.: 2177

Bravo AF: 0.147

Asia WGS AF: 0.272 AC: 946 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.76
DANN	Benign	0.32
PhyloP100		-0.67
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: rs490514; hg19: chr20-41435664;