rs11833635

Positions:

• chr12-70762141-G-A
• chr12-70762141-G-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_002849.4(PTPRR):​c.472-515C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.219 in 151,996 control chromosomes in the GnomAD database, including 3,863 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 0.22 (3863 hom., cov: 32)
• Consequence: PTPRR NM_002849.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.459

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]

LOC124902960 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.283 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
PTPRR	NM_002849.4	c.472-515C>T		intron_variant		ENST00000283228.7	NP_002840.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
PTPRR	ENST00000283228.7	c.472-515C>T		intron_variant		1	NM_002849.4	ENSP00000283228.2
PTPRR	ENST00000342084.8	c.136-515C>T		intron_variant		2		ENSP00000339605.4

Frequencies

GnomAD3 genomes AF: 0.219 AC: 33334 AN: 151878 Hom.: 3858 Cov.: 32

Gnomad AFR AF: 0.287

Gnomad AMI AF: 0.215

Gnomad AMR AF: 0.206

Gnomad ASJ AF: 0.241

Gnomad EAS AF: 0.0968

Gnomad SAS AF: 0.176

Gnomad FIN AF: 0.162

Gnomad MID AF: 0.244

Gnomad NFE AF: 0.201

Gnomad OTH AF: 0.224

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

GnomAD4 genome AF: 0.219 AC: 33360 AN: 151996 Hom.: 3863 Cov.: 32 AF XY: 0.217 AC XY: 16122 AN XY: 74296

Gnomad4 AFR AF: 0.287

Gnomad4 AMR AF: 0.207

Gnomad4 ASJ AF: 0.241

Gnomad4 EAS AF: 0.0968

Gnomad4 SAS AF: 0.176

Gnomad4 FIN AF: 0.162

Gnomad4 NFE AF: 0.201

Gnomad4 OTH AF: 0.222

Alfa AF: 0.188 Hom.: 1711

Bravo AF: 0.224

Asia WGS AF: 0.153 AC: 534 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.6
DANN	Benign	0.53

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

Publications

LitVar

Other links and lift over

dbSNP: rs11833635; hg19: chr12-71155921;