rs6102917

Positions:

• chr20-42590779-C-G
• chr20-42590779-C-T

Variant summary

Our verdict is Benign. Variant got -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

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

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
PTPRT	NM_007050.6	c.1153+87087G>C		intron_variant		ENST00000373187.6	NP_008981.4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
PTPRT	ENST00000373187.6	c.1153+87087G>C		intron_variant		1	NM_007050.6	ENSP00000362283.1
PTPRT	ENST00000373193.7	c.1153+87087G>C		intron_variant		1		ENSP00000362289.4
PTPRT	ENST00000617474.1	n.*1011+87087G>C		intron_variant		5		ENSP00000484248.1

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

Gnomad4 AFR AF: 0.371

Gnomad4 AMR AF: 0.0653

Gnomad4 ASJ AF: 0.0407

Gnomad4 EAS AF: 0.138

Gnomad4 SAS AF: 0.0476

Gnomad4 FIN AF: 0.0131

Gnomad4 NFE AF: 0.0222

Gnomad4 OTH AF: 0.103

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 v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	0.17
DANN	Benign	0.73

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

Publications

LitVar

Other links and lift over

dbSNP: rs6102917; hg19: chr20-41219419;