NM_007050.6:c.215-5891G>C

Variant names:

• chr20-42797357-C-G
• rs6130222
• NM_007050.6:c.215-5891G>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.215-5891G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.412 in 152,098 control chromosomes in the GnomAD database, including 15,207 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 0.41 (15207 hom., cov: 32)
• Consequence: PTPRT NM_007050.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.588
• 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=-0.98).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.536 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PTPRT	NM_007050.6	c.215-5891G>C		intron_variant	Intron 2 of 30	ENST00000373187.6	NP_008981.4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PTPRT	ENST00000373187.6	c.215-5891G>C		intron_variant	Intron 2 of 30	1	NM_007050.6	ENSP00000362283.1
PTPRT	ENST00000373193.7	c.215-5891G>C		intron_variant	Intron 2 of 31	1		ENSP00000362289.4
PTPRT	ENST00000617474.1	n.*73-5891G>C		intron_variant	Intron 2 of 30	5		ENSP00000484248.1

Frequencies

GnomAD3 genomes AF: 0.412 AC: 62640 AN: 151980 Hom.: 15208 Cov.: 32

Gnomad AFR AF: 0.138

Gnomad AMI AF: 0.616

Gnomad AMR AF: 0.409

Gnomad ASJ AF: 0.517

Gnomad EAS AF: 0.534

Gnomad SAS AF: 0.418

Gnomad FIN AF: 0.545

Gnomad MID AF: 0.510

Gnomad NFE AF: 0.541

Gnomad OTH AF: 0.438

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

GnomAD4 genome AF: 0.412 AC: 62646 AN: 152098 Hom.: 15207 Cov.: 32 AF XY: 0.414 AC XY: 30763 AN XY: 74352

African (AFR) AF: 0.137 AC: 5706 AN: 41534

American (AMR) AF: 0.408 AC: 6241 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.517 AC: 1795 AN: 3470

East Asian (EAS) AF: 0.534 AC: 2754 AN: 5154

South Asian (SAS) AF: 0.418 AC: 2017 AN: 4822

European-Finnish (FIN) AF: 0.545 AC: 5762 AN: 10566

Middle Eastern (MID) AF: 0.517 AC: 151 AN: 292

European-Non Finnish (NFE) AF: 0.541 AC: 36734 AN: 67962

Other (OTH) AF: 0.438 AC: 925 AN: 2110

Alfa AF: 0.470 Hom.: 2279

Bravo AF: 0.390

Asia WGS AF: 0.446 AC: 1553 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	1.4
DANN	Benign	0.54
PhyloP100		-0.59
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: rs6130222; hg19: chr20-41425997;