20-42212139-A-G

Variant names:

• chr20-42212139-A-G
• rs7345986
• NM_007050.6:c.2343-12751T>C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_007050.6(PTPRT):​c.2343-12751T>C variant causes a intron change. 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 0.62 (21241 hom., cov: 13)
• Consequence: PTPRT NM_007050.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: No conservation score assigned

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=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.767 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PTPRT	NM_007050.6	c.2343-12751T>C		intron_variant	Intron 15 of 30	ENST00000373187.6	NP_008981.4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PTPRT	ENST00000373187.6	c.2343-12751T>C		intron_variant	Intron 15 of 30	1	NM_007050.6	ENSP00000362283.1
PTPRT	ENST00000373193.7	c.2400-12742T>C		intron_variant	Intron 16 of 31	1		ENSP00000362289.4
PTPRT	ENST00000617474.1	n.*2201-12742T>C		intron_variant	Intron 15 of 30	5		ENSP00000484248.1

Frequencies

GnomAD3 genomes AF: 0.623 AC: 66927 AN: 107482 Hom.: 21232 Cov.: 13

Gnomad AFR AF: 0.776

Gnomad AMI AF: 0.667

Gnomad AMR AF: 0.589

Gnomad ASJ AF: 0.547

Gnomad EAS AF: 0.386

Gnomad SAS AF: 0.459

Gnomad FIN AF: 0.667

Gnomad MID AF: 0.601

Gnomad NFE AF: 0.575

Gnomad OTH AF: 0.604

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

GnomAD4 genome AF: 0.623 AC: 66955 AN: 107542 Hom.: 21241 Cov.: 13 AF XY: 0.622 AC XY: 31102 AN XY: 50012

Gnomad4 AFR AF: 0.776

Gnomad4 AMR AF: 0.589

Gnomad4 ASJ AF: 0.547

Gnomad4 EAS AF: 0.384

Gnomad4 SAS AF: 0.460

Gnomad4 FIN AF: 0.667

Gnomad4 NFE AF: 0.575

Gnomad4 OTH AF: 0.601

Alfa AF: 0.599 Hom.: 1994

Bravo AF: 0.625

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.88
DANN	Benign	0.48

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: rs7345986; hg19: chr20-40840779;