chr20-42581631-A-G

Variant names:

• chr20-42581631-A-G
• rs6016834
• NM_007050.6:c.1153+96235T>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+96235T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.375 in 152,068 control chromosomes in the GnomAD database, including 11,025 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 0.37 (11025 hom., cov: 32)
• Consequence: PTPRT NM_007050.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.902
• Publications: 3 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=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.451 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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PTPRT	NM_007050.6	MANE Select	c.1153+96235T>C		intron	N/A	NP_008981.4
	PTPRT	NM_001394024.1		c.1153+96235T>C		intron	N/A	NP_001380953.1
	PTPRT	NM_133170.4		c.1153+96235T>C		intron	N/A	NP_573400.3

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PTPRT	ENST00000373187.6	TSL:1 MANE Select	c.1153+96235T>C		intron	N/A	ENSP00000362283.1
	PTPRT	ENST00000373193.7	TSL:1	c.1153+96235T>C		intron	N/A	ENSP00000362289.4
	PTPRT	ENST00000373198.8	TSL:1	c.1153+96235T>C		intron	N/A	ENSP00000362294.4

Frequencies

GnomAD3 genomes AF: 0.375 AC: 56958 AN: 151950 Hom.: 11029 Cov.: 32

Gnomad AFR AF: 0.325

Gnomad AMI AF: 0.341

Gnomad AMR AF: 0.267

Gnomad ASJ AF: 0.534

Gnomad EAS AF: 0.466

Gnomad SAS AF: 0.456

Gnomad FIN AF: 0.459

Gnomad MID AF: 0.348

Gnomad NFE AF: 0.396

Gnomad OTH AF: 0.351

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

GnomAD4 genome AF: 0.375 AC: 56966 AN: 152068 Hom.: 11025 Cov.: 32 AF XY: 0.379 AC XY: 28199 AN XY: 74316

African (AFR) AF: 0.325 AC: 13488 AN: 41488

American (AMR) AF: 0.267 AC: 4076 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.534 AC: 1853 AN: 3470

East Asian (EAS) AF: 0.466 AC: 2413 AN: 5176

South Asian (SAS) AF: 0.454 AC: 2188 AN: 4816

European-Finnish (FIN) AF: 0.459 AC: 4848 AN: 10556

Middle Eastern (MID) AF: 0.350 AC: 103 AN: 294

European-Non Finnish (NFE) AF: 0.396 AC: 26947 AN: 67966

Other (OTH) AF: 0.350 AC: 739 AN: 2114

Alfa AF: 0.379 Hom.: 18454

Bravo AF: 0.357

Asia WGS AF: 0.411 AC: 1431 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	8.4
DANN	Benign	0.51
PhyloP100		0.90
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: rs6016834; hg19: chr20-41210271;