20-42225982-G-T

Variant names:

• chr20-42225982-G-T
• rs926647
• NM_007050.6:c.2342+10247C>A

Variant summary

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

The NM_007050.6(PTPRT):​c.2342+10247C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.619 in 152,102 control chromosomes in the GnomAD database, including 29,997 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 0.62 (29997 hom., cov: 33)
• Consequence: PTPRT NM_007050.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.130
• 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=-1.02).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.759 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PTPRT	NM_007050.6	c.2342+10247C>A		intron_variant	Intron 15 of 30	ENST00000373187.6	NP_008981.4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PTPRT	ENST00000373187.6	c.2342+10247C>A		intron_variant	Intron 15 of 30	1	NM_007050.6	ENSP00000362283.1
PTPRT	ENST00000373193.7	c.2399+10247C>A		intron_variant	Intron 16 of 31	1		ENSP00000362289.4
PTPRT	ENST00000617474.1	n.*2200+10247C>A		intron_variant	Intron 15 of 30	5		ENSP00000484248.1

Frequencies

GnomAD3 genomes AF: 0.619 AC: 94013 AN: 151984 Hom.: 29971 Cov.: 33

Gnomad AFR AF: 0.766

Gnomad AMI AF: 0.676

Gnomad AMR AF: 0.554

Gnomad ASJ AF: 0.552

Gnomad EAS AF: 0.371

Gnomad SAS AF: 0.467

Gnomad FIN AF: 0.672

Gnomad MID AF: 0.573

Gnomad NFE AF: 0.568

Gnomad OTH AF: 0.601

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

GnomAD4 genome AF: 0.619 AC: 94083 AN: 152102 Hom.: 29997 Cov.: 33 AF XY: 0.617 AC XY: 45881 AN XY: 74350

African (AFR) AF: 0.766 AC: 31811 AN: 41506

American (AMR) AF: 0.553 AC: 8454 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.552 AC: 1915 AN: 3470

East Asian (EAS) AF: 0.370 AC: 1911 AN: 5160

South Asian (SAS) AF: 0.467 AC: 2256 AN: 4832

European-Finnish (FIN) AF: 0.672 AC: 7099 AN: 10568

Middle Eastern (MID) AF: 0.558 AC: 164 AN: 294

European-Non Finnish (NFE) AF: 0.568 AC: 38595 AN: 67962

Other (OTH) AF: 0.597 AC: 1263 AN: 2114

Alfa AF: 0.596 Hom.: 3525

Bravo AF: 0.616

Asia WGS AF: 0.458 AC: 1600 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.3
DANN	Benign	0.39
PhyloP100		0.13
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: rs926647; hg19: chr20-40854622;