chr12-70764673-G-A
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2
The NM_002849.4(PTPRR):c.463C>T(p.Arg155Cys) variant causes a missense change. The variant allele was found at a frequency of 0.00427 in 1,611,368 control chromosomes in the GnomAD database, including 21 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.0032 ( 3 hom., cov: 32)
Exomes 𝑓: 0.0044 ( 18 hom. )
Consequence
PTPRR
NM_002849.4 missense
NM_002849.4 missense
Scores
3
6
10
Clinical Significance
Conservation
PhyloP100: 4.72
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]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -10 ACMG points.
BP4
?
Computational evidence support a benign effect (MetaRNN=0.011015803).
BP6
?
Variant 12-70764673-G-A is Benign according to our data. Variant chr12-70764673-G-A is described in ClinVar as [Benign]. Clinvar id is 718454.Status of the report is criteria_provided_single_submitter, 1 stars.
BS2
?
High Homozygotes in GnomAd at 3 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PTPRR | NM_002849.4 | c.463C>T | p.Arg155Cys | missense_variant | 3/14 | ENST00000283228.7 | |
LOC124902960 | XR_007063361.1 | n.629-8764G>A | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PTPRR | ENST00000283228.7 | c.463C>T | p.Arg155Cys | missense_variant | 3/14 | 1 | NM_002849.4 | P3 | |
PTPRR | ENST00000342084.8 | c.127C>T | p.Arg43Cys | missense_variant | 2/13 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.00325 AC: 494AN: 152134Hom.: 3 Cov.: 32
GnomAD3 genomes
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GnomAD3 exomes AF: 0.00311 AC: 783AN: 251436Hom.: 4 AF XY: 0.00319 AC XY: 433AN XY: 135892
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GnomAD4 exome AF: 0.00437 AC: 6382AN: 1459116Hom.: 18 Cov.: 31 AF XY: 0.00421 AC XY: 3055AN XY: 726120
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GnomAD4 genome ? AF: 0.00324 AC: 494AN: 152252Hom.: 3 Cov.: 32 AF XY: 0.00312 AC XY: 232AN XY: 74444
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | May 31, 2018 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Uncertain
Cadd
Pathogenic
Dann
Pathogenic
DEOGEN2
Benign
T;.
Eigen
Uncertain
Eigen_PC
Uncertain
FATHMM_MKL
Uncertain
D
LIST_S2
Uncertain
D;D
M_CAP
Benign
D
MetaRNN
Benign
T;T
MetaSVM
Benign
T
MutationAssessor
Benign
L;.
MutationTaster
Benign
D;D
PrimateAI
Uncertain
T
PROVEAN
Benign
N;N
REVEL
Benign
Sift
Pathogenic
D;D
Sift4G
Pathogenic
D;D
Polyphen
D;.
Vest4
MVP
MPC
ClinPred
T
GERP RS
Varity_R
gMVP
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at