chr20-42353047-T-C

Variant names:

• chr20-42353047-T-C
• rs6072693
• NM_007050.6:c.1561-762A>G

Variant summary

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

The NM_007050.6(PTPRT):​c.1561-762A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.114 in 152,228 control chromosomes in the GnomAD database, including 1,290 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 0.11 (1290 hom., cov: 33)
• Consequence: PTPRT NM_007050.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.400
• 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=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.21 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_007050.6. 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.1561-762A>G		intron	N/A	NP_008981.4
	PTPRT	NM_001394024.1		c.1561-762A>G		intron	N/A	NP_001380953.1
	PTPRT	NM_133170.4		c.1561-762A>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.1561-762A>G		intron	N/A	ENSP00000362283.1
	PTPRT	ENST00000373193.7	TSL:1	c.1561-762A>G		intron	N/A	ENSP00000362289.4
	PTPRT	ENST00000373198.8	TSL:1	c.1561-762A>G		intron	N/A	ENSP00000362294.4

Frequencies

GnomAD3 genomes AF: 0.114 AC: 17338 AN: 152110 Hom.: 1286 Cov.: 33

Gnomad AFR AF: 0.214

Gnomad AMI AF: 0.0373

Gnomad AMR AF: 0.0787

Gnomad ASJ AF: 0.0518

Gnomad EAS AF: 0.00481

Gnomad SAS AF: 0.0929

Gnomad FIN AF: 0.0946

Gnomad MID AF: 0.0665

Gnomad NFE AF: 0.0787

Gnomad OTH AF: 0.0999

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

GnomAD4 genome AF: 0.114 AC: 17361 AN: 152228 Hom.: 1290 Cov.: 33 AF XY: 0.113 AC XY: 8429 AN XY: 74430

African (AFR) AF: 0.214 AC: 8882 AN: 41490

American (AMR) AF: 0.0785 AC: 1202 AN: 15306

Ashkenazi Jewish (ASJ) AF: 0.0518 AC: 180 AN: 3472

East Asian (EAS) AF: 0.00482 AC: 25 AN: 5190

South Asian (SAS) AF: 0.0927 AC: 447 AN: 4820

European-Finnish (FIN) AF: 0.0946 AC: 1004 AN: 10614

Middle Eastern (MID) AF: 0.0748 AC: 22 AN: 294

European-Non Finnish (NFE) AF: 0.0788 AC: 5357 AN: 68016

Other (OTH) AF: 0.0984 AC: 208 AN: 2114

Alfa AF: 0.0889 Hom.: 1181

Bravo AF: 0.116

Asia WGS AF: 0.0630 AC: 218 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.87
DANN	Benign	0.36
PhyloP100		-0.40
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: rs6072693; hg19: chr20-40981687;