chr20-42354307-C-T

Variant names:

• chr20-42354307-C-T
• rs6016759
• NM_007050.6:c.1561-2022G>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.1561-2022G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.482 in 151,866 control chromosomes in the GnomAD database, including 18,637 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 0.48 (18637 hom., cov: 31)
• Consequence: PTPRT NM_007050.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.748
• Publications: 2 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=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.558 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PTPRT	NM_007050.6	c.1561-2022G>A		intron_variant	Intron 9 of 30	ENST00000373187.6	NP_008981.4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PTPRT	ENST00000373187.6	c.1561-2022G>A		intron_variant	Intron 9 of 30	1	NM_007050.6	ENSP00000362283.1
PTPRT	ENST00000373193.7	c.1561-2022G>A		intron_variant	Intron 9 of 31	1		ENSP00000362289.4
PTPRT	ENST00000617474.1	n.*1419-2022G>A		intron_variant	Intron 9 of 30	5		ENSP00000484248.1

Frequencies

GnomAD3 genomes AF: 0.483 AC: 73258 AN: 151748 Hom.: 18635 Cov.: 31

Gnomad AFR AF: 0.367

Gnomad AMI AF: 0.464

Gnomad AMR AF: 0.485

Gnomad ASJ AF: 0.652

Gnomad EAS AF: 0.136

Gnomad SAS AF: 0.369

Gnomad FIN AF: 0.584

Gnomad MID AF: 0.535

Gnomad NFE AF: 0.563

Gnomad OTH AF: 0.493

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

GnomAD4 genome AF: 0.482 AC: 73270 AN: 151866 Hom.: 18637 Cov.: 31 AF XY: 0.480 AC XY: 35628 AN XY: 74222

African (AFR) AF: 0.367 AC: 15187 AN: 41412

American (AMR) AF: 0.485 AC: 7392 AN: 15248

Ashkenazi Jewish (ASJ) AF: 0.652 AC: 2261 AN: 3470

East Asian (EAS) AF: 0.136 AC: 700 AN: 5162

South Asian (SAS) AF: 0.369 AC: 1773 AN: 4802

European-Finnish (FIN) AF: 0.584 AC: 6140 AN: 10520

Middle Eastern (MID) AF: 0.520 AC: 153 AN: 294

European-Non Finnish (NFE) AF: 0.562 AC: 38217 AN: 67944

Other (OTH) AF: 0.487 AC: 1027 AN: 2108

Alfa AF: 0.535 Hom.: 93867

Bravo AF: 0.468

Asia WGS AF: 0.278 AC: 968 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.24
DANN	Benign	0.58
PhyloP100		-0.75
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: rs6016759; hg19: chr20-40982947;