20-42688304-T-G

Variant names:

• chr20-42688304-T-G
• rs2425524
• ENST00000457704.2:n.1737T>G

Variant summary

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

The ENST00000457704.2(ENSG00000229042):​n.1737T>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.489 in 152,004 control chromosomes in the GnomAD database, including 20,733 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 0.49 (20732 hom., cov: 33)
  • Exomes 𝑓: 0.33 (1 hom.)
• Consequence: ENSG00000229042 ENST00000457704.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.132
• Publications: 1 publications found

Genes affected

ENSG00000229042 (HGNC:):

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=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.772 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000457704.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PTPRT	NM_007050.6	MANE Select	c.860-10145A>C		intron	N/A	NP_008981.4
	LOC101927159	NR_110004.1		n.1737T>G		non_coding_transcript_exon	Exon 4 of 4
	PTPRT	NM_001394024.1		c.860-10145A>C		intron	N/A	NP_001380953.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000229042	ENST00000457704.2	TSL:1	n.1737T>G		non_coding_transcript_exon	Exon 4 of 4
	PTPRT	ENST00000373187.6	TSL:1 MANE Select	c.860-10145A>C		intron	N/A	ENSP00000362283.1
	PTPRT	ENST00000373193.7	TSL:1	c.860-10145A>C		intron	N/A	ENSP00000362289.4

Frequencies

GnomAD3 genomes AF: 0.488 AC: 74163 AN: 151850 Hom.: 20673 Cov.: 33

Gnomad AFR AF: 0.779

Gnomad AMI AF: 0.206

Gnomad AMR AF: 0.433

Gnomad ASJ AF: 0.363

Gnomad EAS AF: 0.418

Gnomad SAS AF: 0.370

Gnomad FIN AF: 0.399

Gnomad MID AF: 0.424

Gnomad NFE AF: 0.364

Gnomad OTH AF: 0.444

GnomAD4 exome AF: 0.333 AC: 12 AN: 36 Hom.: 1 Cov.: 0 AF XY: 0.286 AC XY: 8 AN XY: 28

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AF: 0.500 AC: 1 AN: 2

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.286 AC: 8 AN: 28

Other (OTH) AF: 0.500 AC: 3 AN: 6

GnomAD4 genome AF: 0.489 AC: 74292 AN: 151968 Hom.: 20732 Cov.: 33 AF XY: 0.486 AC XY: 36062 AN XY: 74266

African (AFR) AF: 0.779 AC: 32295 AN: 41462

American (AMR) AF: 0.432 AC: 6608 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.363 AC: 1259 AN: 3468

East Asian (EAS) AF: 0.420 AC: 2161 AN: 5146

South Asian (SAS) AF: 0.371 AC: 1785 AN: 4812

European-Finnish (FIN) AF: 0.399 AC: 4215 AN: 10558

Middle Eastern (MID) AF: 0.442 AC: 130 AN: 294

European-Non Finnish (NFE) AF: 0.364 AC: 24711 AN: 67920

Other (OTH) AF: 0.445 AC: 940 AN: 2114

Alfa AF: 0.315 Hom.: 977

Bravo AF: 0.504

Asia WGS AF: 0.383 AC: 1332 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	3.7
DANN	Benign	0.61
PhyloP100		-0.13
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: rs2425524; hg19: chr20-41316944;