chr20-42532838-A-G

Variant names:

• chr20-42532838-A-G
• rs986831
• NM_007050.6:c.1154-60276T>C

Variant summary

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

The NM_007050.6(PTPRT):​c.1154-60276T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.5 in 151,808 control chromosomes in the GnomAD database, including 21,864 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 0.50 (21864 hom., cov: 31)
• Consequence: PTPRT NM_007050.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.288
• Publications: 3 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 (EAS) allele frequency at 95% confidence interval = 0.66 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PTPRT	NM_007050.6	c.1154-60276T>C		intron_variant	Intron 7 of 30	ENST00000373187.6	NP_008981.4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PTPRT	ENST00000373187.6	c.1154-60276T>C		intron_variant	Intron 7 of 30	1	NM_007050.6	ENSP00000362283.1
PTPRT	ENST00000373193.7	c.1154-60276T>C		intron_variant	Intron 7 of 31	1		ENSP00000362289.4
PTPRT	ENST00000617474.1	n.*1012-60276T>C		intron_variant	Intron 7 of 30	5		ENSP00000484248.1

Frequencies

GnomAD3 genomes AF: 0.501 AC: 75947 AN: 151690 Hom.: 21860 Cov.: 31

Gnomad AFR AF: 0.202

Gnomad AMI AF: 0.707

Gnomad AMR AF: 0.625

Gnomad ASJ AF: 0.497

Gnomad EAS AF: 0.679

Gnomad SAS AF: 0.527

Gnomad FIN AF: 0.621

Gnomad MID AF: 0.500

Gnomad NFE AF: 0.617

Gnomad OTH AF: 0.520

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

GnomAD4 genome AF: 0.500 AC: 75970 AN: 151808 Hom.: 21864 Cov.: 31 AF XY: 0.504 AC XY: 37377 AN XY: 74156

African (AFR) AF: 0.202 AC: 8362 AN: 41398

American (AMR) AF: 0.625 AC: 9543 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.497 AC: 1726 AN: 3470

East Asian (EAS) AF: 0.678 AC: 3457 AN: 5096

South Asian (SAS) AF: 0.528 AC: 2534 AN: 4802

European-Finnish (FIN) AF: 0.621 AC: 6549 AN: 10546

Middle Eastern (MID) AF: 0.480 AC: 141 AN: 294

European-Non Finnish (NFE) AF: 0.617 AC: 41912 AN: 67920

Other (OTH) AF: 0.524 AC: 1103 AN: 2106

Alfa AF: 0.510 Hom.: 3270

Bravo AF: 0.491

Asia WGS AF: 0.582 AC: 2022 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	2.6
DANN	Benign	0.48
PhyloP100		0.29
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: rs986831; hg19: chr20-41161478;