NM_007050.6:c.1153+87087G>C

Variant names:

• chr20-42590779-C-G
• rs6102917
• NM_007050.6:c.1153+87087G>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.1153+87087G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.127 in 151,952 control chromosomes in the GnomAD database, including 3,022 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 0.13 (3022 hom., cov: 32)
• Consequence: PTPRT NM_007050.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.58
• Publications: 5 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=-0.83).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.366 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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PTPRT	NM_007050.6	MANE Select	c.1153+87087G>C		intron	N/A	NP_008981.4
	PTPRT	NM_001394024.1		c.1153+87087G>C		intron	N/A	NP_001380953.1
	PTPRT	NM_133170.4		c.1153+87087G>C		intron	N/A	NP_573400.3

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PTPRT	ENST00000373187.6	TSL:1 MANE Select	c.1153+87087G>C		intron	N/A	ENSP00000362283.1	O14522-3
	PTPRT	ENST00000373193.7	TSL:1	c.1153+87087G>C		intron	N/A	ENSP00000362289.4	O14522-1
	PTPRT	ENST00000373198.8	TSL:1	c.1153+87087G>C		intron	N/A	ENSP00000362294.4	A0A075B6H0

Frequencies

GnomAD3 genomes AF: 0.127 AC: 19288 AN: 151836 Hom.: 3017 Cov.: 32

Gnomad AFR AF: 0.371

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0652

Gnomad ASJ AF: 0.0407

Gnomad EAS AF: 0.138

Gnomad SAS AF: 0.0475

Gnomad FIN AF: 0.0131

Gnomad MID AF: 0.0728

Gnomad NFE AF: 0.0222

Gnomad OTH AF: 0.105

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

GnomAD4 genome AF: 0.127 AC: 19316 AN: 151952 Hom.: 3022 Cov.: 32 AF XY: 0.123 AC XY: 9134 AN XY: 74296

African (AFR) AF: 0.371 AC: 15345 AN: 41380

American (AMR) AF: 0.0653 AC: 996 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.0407 AC: 141 AN: 3468

East Asian (EAS) AF: 0.138 AC: 714 AN: 5172

South Asian (SAS) AF: 0.0476 AC: 229 AN: 4812

European-Finnish (FIN) AF: 0.0131 AC: 139 AN: 10574

Middle Eastern (MID) AF: 0.0782 AC: 23 AN: 294

European-Non Finnish (NFE) AF: 0.0222 AC: 1512 AN: 67970

Other (OTH) AF: 0.103 AC: 217 AN: 2112

Alfa AF: 0.0840 Hom.: 253

Bravo AF: 0.142

Asia WGS AF: 0.0850 AC: 295 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	0.17
DANN	Benign	0.73
PhyloP100		-1.6
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: rs6102917; hg19: chr20-41219419;