NM_002849.4:c.59-2799C>T

Variant names:

• chr12-70895776-G-A
• rs4760854
• NM_002849.4:c.59-2799C>T

Variant summary

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

The NM_002849.4(PTPRR):​c.59-2799C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.728 in 151,384 control chromosomes in the GnomAD database, including 40,281 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 0.73 (40281 hom., cov: 31)
• Consequence: PTPRR NM_002849.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.215
• Publications: 7 publications found

Genes affected

PTPRR (HGNC:9680): (protein tyrosine phosphatase receptor type R) 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 a single intracellular catalytic domain, and thus represents a receptor-type PTP. Silencing of this gene has been associated with colorectal cancer. Multiple transcript variants encoding different isoforms have been found for this gene. This gene shares a symbol (PTPRQ) with another gene, protein tyrosine phosphatase, receptor type, Q (GeneID 374462), which is also located on chromosome 12. [provided by RefSeq, May 2011]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.743 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PTPRR	NM_002849.4	c.59-2799C>T		intron_variant	Intron 1 of 13	ENST00000283228.7	NP_002840.2
PTPRR	XM_011538615.3	c.35-2799C>T		intron_variant	Intron 1 of 13		XP_011536917.1
PTPRR	XM_047429233.1	c.59-2799C>T		intron_variant	Intron 1 of 11		XP_047285189.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PTPRR	ENST00000283228.7	c.59-2799C>T		intron_variant	Intron 1 of 13	1	NM_002849.4	ENSP00000283228.2

Frequencies

GnomAD3 genomes AF: 0.728 AC: 110158 AN: 151264 Hom.: 40229 Cov.: 31

Gnomad AFR AF: 0.749

Gnomad AMI AF: 0.846

Gnomad AMR AF: 0.736

Gnomad ASJ AF: 0.714

Gnomad EAS AF: 0.615

Gnomad SAS AF: 0.588

Gnomad FIN AF: 0.655

Gnomad MID AF: 0.703

Gnomad NFE AF: 0.743

Gnomad OTH AF: 0.717

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

GnomAD4 genome AF: 0.728 AC: 110267 AN: 151384 Hom.: 40281 Cov.: 31 AF XY: 0.722 AC XY: 53428 AN XY: 73984

African (AFR) AF: 0.750 AC: 31027 AN: 41388

American (AMR) AF: 0.735 AC: 11126 AN: 15132

Ashkenazi Jewish (ASJ) AF: 0.714 AC: 2463 AN: 3448

East Asian (EAS) AF: 0.615 AC: 3150 AN: 5124

South Asian (SAS) AF: 0.589 AC: 2837 AN: 4820

European-Finnish (FIN) AF: 0.655 AC: 6928 AN: 10570

Middle Eastern (MID) AF: 0.704 AC: 207 AN: 294

European-Non Finnish (NFE) AF: 0.743 AC: 50251 AN: 67596

Other (OTH) AF: 0.717 AC: 1506 AN: 2100

Alfa AF: 0.740 Hom.: 132542

Bravo AF: 0.741

Asia WGS AF: 0.593 AC: 2059 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	2.1
DANN	Benign	0.53
PhyloP100		0.21
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: rs4760854; hg19: chr12-71289556;