rs6102794

Variant names:

• chr20-42352362-C-A
• rs6102794
• NM_007050.6:c.1561-77G>T

Your query was ambiguous. Multiple possible variants found:

• chr20-42352362-C-A
• chr20-42352362-C-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.1561-77G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.273 in 1,468,512 control chromosomes in the GnomAD database, including 59,170 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as (no stars).

• Frequency:
  • Genomes: 𝑓 0.23 (4753 hom., cov: 32)
  • Exomes 𝑓: 0.28 (54417 hom.)
• Consequence: PTPRT NM_007050.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.61
• Publications: 4 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 (NFE) allele frequency at 95% confidence interval = 0.301 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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PTPRT	NM_007050.6	MANE Select	c.1561-77G>T		intron	N/A	NP_008981.4
	PTPRT	NM_001394024.1		c.1561-77G>T		intron	N/A	NP_001380953.1
	PTPRT	NM_133170.4		c.1561-77G>T		intron	N/A	NP_573400.3

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PTPRT	ENST00000373187.6	TSL:1 MANE Select	c.1561-77G>T		intron	N/A	ENSP00000362283.1	O14522-3
	PTPRT	ENST00000373193.7	TSL:1	c.1561-77G>T		intron	N/A	ENSP00000362289.4	O14522-1
	PTPRT	ENST00000373198.8	TSL:1	c.1561-77G>T		intron	N/A	ENSP00000362294.4	A0A075B6H0

Frequencies

GnomAD3 genomes AF: 0.226 AC: 34404 AN: 151980 Hom.: 4751 Cov.: 32

Gnomad AFR AF: 0.0849

Gnomad AMI AF: 0.180

Gnomad AMR AF: 0.268

Gnomad ASJ AF: 0.325

Gnomad EAS AF: 0.0367

Gnomad SAS AF: 0.100

Gnomad FIN AF: 0.336

Gnomad MID AF: 0.225

Gnomad NFE AF: 0.305

Gnomad OTH AF: 0.224

GnomAD4 exome AF: 0.278 AC: 366374 AN: 1316414 Hom.: 54417 AF XY: 0.273 AC XY: 180088 AN XY: 659400

African (AFR) AF: 0.0804 AC: 2426 AN: 30184

American (AMR) AF: 0.294 AC: 12699 AN: 43232

Ashkenazi Jewish (ASJ) AF: 0.323 AC: 7885 AN: 24388

East Asian (EAS) AF: 0.0718 AC: 2782 AN: 38744

South Asian (SAS) AF: 0.112 AC: 9136 AN: 81304

European-Finnish (FIN) AF: 0.331 AC: 16960 AN: 51254

Middle Eastern (MID) AF: 0.230 AC: 1004 AN: 4366

European-Non Finnish (NFE) AF: 0.303 AC: 299252 AN: 987580

Other (OTH) AF: 0.257 AC: 14230 AN: 55362

GnomAD4 genome AF: 0.226 AC: 34412 AN: 152098 Hom.: 4753 Cov.: 32 AF XY: 0.224 AC XY: 16662 AN XY: 74346

African (AFR) AF: 0.0851 AC: 3532 AN: 41502

American (AMR) AF: 0.268 AC: 4099 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.325 AC: 1129 AN: 3470

East Asian (EAS) AF: 0.0366 AC: 189 AN: 5164

South Asian (SAS) AF: 0.100 AC: 482 AN: 4808

European-Finnish (FIN) AF: 0.336 AC: 3558 AN: 10576

Middle Eastern (MID) AF: 0.214 AC: 63 AN: 294

European-Non Finnish (NFE) AF: 0.305 AC: 20728 AN: 67976

Other (OTH) AF: 0.221 AC: 468 AN: 2114

Alfa AF: 0.269 Hom.: 11546

Bravo AF: 0.218

Asia WGS AF: 0.0910 AC: 317 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	0.30
DANN	Benign	0.34
PhyloP100		-1.6
Mutation Taster		=12/88	disease causing

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: rs6102794; hg19: chr20-40981002;