rs11833635

Variant names:

• chr12-70762141-G-A
• rs11833635
• NM_002849.4:c.472-515C>T

Your query was ambiguous. Multiple possible variants found:

• chr12-70762141-G-A
• chr12-70762141-G-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.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
• Publications: 3 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]

ENSG00000307941 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_002849.4. 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
	PTPRR	NM_002849.4	MANE Select	c.472-515C>T		intron	N/A	NP_002840.2	Q15256-1
	PTPRR	NM_001207015.2		c.136-515C>T		intron	N/A	NP_001193944.1	Q15256-5

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PTPRR	ENST00000283228.7	TSL:1 MANE Select	c.472-515C>T		intron	N/A	ENSP00000283228.2	Q15256-1
	PTPRR	ENST00000342084.8	TSL:2	c.136-515C>T		intron	N/A	ENSP00000339605.4	Q15256-5
	ENSG00000307941	ENST00000829948.1		n.73-11296G>A		intron	N/A

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

African (AFR) AF: 0.287 AC: 11891 AN: 41424

American (AMR) AF: 0.207 AC: 3158 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.241 AC: 836 AN: 3470

East Asian (EAS) AF: 0.0968 AC: 502 AN: 5184

South Asian (SAS) AF: 0.176 AC: 844 AN: 4808

European-Finnish (FIN) AF: 0.162 AC: 1715 AN: 10554

Middle Eastern (MID) AF: 0.245 AC: 72 AN: 294

European-Non Finnish (NFE) AF: 0.201 AC: 13676 AN: 67956

Other (OTH) AF: 0.222 AC: 470 AN: 2114

Alfa AF: 0.195 Hom.: 2391

Bravo AF: 0.224

Asia WGS AF: 0.153 AC: 534 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.6
DANN	Benign	0.53
PhyloP100		-0.46
Mutation Taster		=99/1	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: rs11833635; hg19: chr12-71155921;