NM_002834.5(PTPN11):c.854-32A>C AND not provided

Germline classification:: Benign (2 submissions)
Last evaluated:: Jun 3, 2016
Review status:: 2 stars out of maximum of 4 stars
criteria provided, multiple submitters, no conflicts

Somatic classification of clinical impact:: None
Review status:: (0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided

Somatic classification of oncogenicity:: None
Review status:: (0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided

Record status:: current
Accession:: RCV000680300.2

Allele description [Variation Report for NM_002834.5(PTPN11):c.854-32A>C]

NM_002834.5(PTPN11):c.854-32A>C

Gene:

PTPN11:protein tyrosine phosphatase non-receptor type 11 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

12q24.13

Genomic location:

Preferred name:

NM_002834.5(PTPN11):c.854-32A>C

HGVS:

NC_000012.12:g.112477619A>C
NG_007459.1:g.63888A>C
NM_001330437.2:c.854-32A>C
NM_001374625.1:c.851-32A>C
NM_002834.5:c.854-32A>CMANE SELECT
NM_080601.3:c.854-32A>C
LRG_614t1:c.854-32A>C
LRG_614:g.63888A>C
NC_000012.11:g.112915423A>C
NM_002834.3:c.854-32A>C
c.854-32A>C

Links:

dbSNP: rs187389813

NCBI 1000 Genomes Browser:

rs187389813

Molecular consequence:

NM_001330437.2:c.854-32A>C - intron variant - [Sequence Ontology: SO:0001627]
NM_001374625.1:c.851-32A>C - intron variant - [Sequence Ontology: SO:0001627]
NM_002834.5:c.854-32A>C - intron variant - [Sequence Ontology: SO:0001627]
NM_080601.3:c.854-32A>C - intron variant - [Sequence Ontology: SO:0001627]

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

Recent activity

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Klebsiella quasipneumoniae strain:H20-3
Klebsiella quasipneumoniae strain:H20-3
Klebsiella quasipneumoniae strain:H20-3 Genome sequencing

BioProject
Soroseris glomerata internal transcribed spacer 1, partial sequence; 5.8S riboso...
Soroseris glomerata internal transcribed spacer 1, partial sequence; 5.8S ribosomal RNA gene, complete sequence; and internal transcribed spacer 2, partial sequence
gi|170284065|gb|EU363656.1|

Nucleotide
Mus musculus bone marrow macrophage cDNA, RIKEN full-length enriched library, cl...
Mus musculus bone marrow macrophage cDNA, RIKEN full-length enriched library, clone:I830077J02 product:weakly similar to BA552M11.4.1 (Novel protein (Isoform 1)) (Fragment) [Homo sapiens], full insert sequence
gi|74220181|dbj|AK152510.1|

Nucleotide
PREDICTED: Homo sapiens lysine acetyltransferase 6B (KAT6B), transcript variant ...
PREDICTED: Homo sapiens lysine acetyltransferase 6B (KAT6B), transcript variant X15, mRNA
gi|2462497506|ref|XM_054331606.1|

Nucleotide
histone acetyltransferase KAT6B isoform X4 [Homo sapiens]
histone acetyltransferase KAT6B isoform X4 [Homo sapiens]
gi|2462497503|ref|XP_054187579.1|

Protein

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000514320	GeneDx	criteria provided, single submitter (GeneDx Variant Classification (06012015))	Benign (Jun 3, 2016)	germline	clinical testing	Citation Link,
SCV005231501	Breakthrough Genomics, Breakthrough Genomics	criteria provided, single submitter (ACMG Guidelines, 2015)	Benign	germline	not provided	PubMed (1) [See all records that cite this PMID]

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000514320

GeneDx

criteria provided, single submitter

(GeneDx Variant Classification (06012015))

Benign
(Jun 3, 2016)

germline

clinical testing

Citation Link,

SCV005231501

Breakthrough Genomics, Breakthrough Genomics

criteria provided, single submitter

(ACMG Guidelines, 2015)

Benign

germline

not provided

PubMed (1)
[See all records that cite this PMID]

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	yes	not provided	not provided	not provided	not provided	not provided	clinical testing, not provided

Citations

PubMed

Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology.

Richards S, Aziz N, Bale S, Bick D, Das S, Gastier-Foster J, Grody WW, Hegde M, Lyon E, Spector E, Voelkerding K, Rehm HL; ACMG Laboratory Quality Assurance Committee..

Genet Med. 2015 May;17(5):405-24. doi: 10.1038/gim.2015.30. Epub 2015 Mar 5.

PubMed [citation]

PMID:: 25741868
PMCID:: PMC4544753

Details of each submission

From GeneDx, SCV000514320.5

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	not provided

Description

This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease.

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	yes	not provided	not provided	not provided		not provided	not provided	not provided	not provided

From Breakthrough Genomics, Breakthrough Genomics, SCV005231501.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	not provided	PubMed (1)

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	yes	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Sep 29, 2024

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