chr20-42450590-C-T

Variant names:

• chr20-42450590-C-T
• rs6130134
• NM_007050.6:c.1451-2261G>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.1451-2261G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.222 in 152,016 control chromosomes in the GnomAD database, including 3,809 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 0.22 (3809 hom., cov: 32)
• Consequence: PTPRT NM_007050.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.813
• 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=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.295 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PTPRT	NM_007050.6	c.1451-2261G>A		intron_variant	Intron 8 of 30	ENST00000373187.6	NP_008981.4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PTPRT	ENST00000373187.6	c.1451-2261G>A		intron_variant	Intron 8 of 30	1	NM_007050.6	ENSP00000362283.1
PTPRT	ENST00000373193.7	c.1451-2261G>A		intron_variant	Intron 8 of 31	1		ENSP00000362289.4
PTPRT	ENST00000617474.1	n.*1309-2261G>A		intron_variant	Intron 8 of 30	5		ENSP00000484248.1

Frequencies

GnomAD3 genomes AF: 0.222 AC: 33675 AN: 151900 Hom.: 3804 Cov.: 32

Gnomad AFR AF: 0.204

Gnomad AMI AF: 0.0493

Gnomad AMR AF: 0.224

Gnomad ASJ AF: 0.283

Gnomad EAS AF: 0.308

Gnomad SAS AF: 0.239

Gnomad FIN AF: 0.211

Gnomad MID AF: 0.306

Gnomad NFE AF: 0.224

Gnomad OTH AF: 0.255

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

GnomAD4 genome AF: 0.222 AC: 33699 AN: 152016 Hom.: 3809 Cov.: 32 AF XY: 0.222 AC XY: 16475 AN XY: 74282

African (AFR) AF: 0.204 AC: 8443 AN: 41468

American (AMR) AF: 0.224 AC: 3416 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.283 AC: 982 AN: 3466

East Asian (EAS) AF: 0.308 AC: 1590 AN: 5164

South Asian (SAS) AF: 0.239 AC: 1152 AN: 4816

European-Finnish (FIN) AF: 0.211 AC: 2221 AN: 10540

Middle Eastern (MID) AF: 0.318 AC: 93 AN: 292

European-Non Finnish (NFE) AF: 0.224 AC: 15222 AN: 67974

Other (OTH) AF: 0.253 AC: 535 AN: 2112

Alfa AF: 0.221 Hom.: 476

Bravo AF: 0.222

Asia WGS AF: 0.260 AC: 903 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	9.8
DANN	Benign	0.77
PhyloP100		-0.81
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: rs6130134; hg19: chr20-41079230;