chr20-42183140-C-A

Variant names:

• chr20-42183140-C-A
• rs7262414
• NM_007050.6:c.2491+16100G>T

Variant summary

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

The NM_007050.6(PTPRT):​c.2491+16100G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.157 in 152,128 control chromosomes in the GnomAD database, including 2,189 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 0.16 (2189 hom., cov: 32)
• Consequence: PTPRT NM_007050.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.671
• Publications: 8 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=-0.8).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.198 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PTPRT	NM_007050.6	c.2491+16100G>T		intron_variant	Intron 16 of 30	ENST00000373187.6	NP_008981.4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PTPRT	ENST00000373187.6	c.2491+16100G>T		intron_variant	Intron 16 of 30	1	NM_007050.6	ENSP00000362283.1
PTPRT	ENST00000373193.7	c.2557+16100G>T		intron_variant	Intron 17 of 31	1		ENSP00000362289.4
PTPRT	ENST00000617474.1	n.*2358+16100G>T		intron_variant	Intron 16 of 30	5		ENSP00000484248.1

Frequencies

GnomAD3 genomes AF: 0.157 AC: 23832 AN: 152010 Hom.: 2192 Cov.: 32

Gnomad AFR AF: 0.100

Gnomad AMI AF: 0.380

Gnomad AMR AF: 0.132

Gnomad ASJ AF: 0.164

Gnomad EAS AF: 0.00635

Gnomad SAS AF: 0.144

Gnomad FIN AF: 0.191

Gnomad MID AF: 0.171

Gnomad NFE AF: 0.201

Gnomad OTH AF: 0.151

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

GnomAD4 genome AF: 0.157 AC: 23831 AN: 152128 Hom.: 2189 Cov.: 32 AF XY: 0.153 AC XY: 11383 AN XY: 74370

African (AFR) AF: 0.100 AC: 4158 AN: 41498

American (AMR) AF: 0.132 AC: 2013 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.164 AC: 569 AN: 3468

East Asian (EAS) AF: 0.00617 AC: 32 AN: 5184

South Asian (SAS) AF: 0.144 AC: 692 AN: 4816

European-Finnish (FIN) AF: 0.191 AC: 2018 AN: 10582

Middle Eastern (MID) AF: 0.167 AC: 49 AN: 294

European-Non Finnish (NFE) AF: 0.201 AC: 13639 AN: 67984

Other (OTH) AF: 0.149 AC: 315 AN: 2108

Alfa AF: 0.183 Hom.: 4917

Bravo AF: 0.148

Asia WGS AF: 0.0790 AC: 278 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	0.93
DANN	Benign	0.76
PhyloP100		-0.67
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: rs7262414; hg19: chr20-40811780;