NM_001253852.3(AP4B1):c.618-13G>C AND not specified

Germline classification:: Benign/Likely benign (4 submissions)
Last evaluated:: Jan 22, 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:: RCV000145023.12

Allele description [Variation Report for NM_001253852.3(AP4B1):c.618-13G>C]

NM_001253852.3(AP4B1):c.618-13G>C

Genes:

AP4B1-AS1:AP4B1 antisense RNA 1 [Gene - HGNC]
AP4B1:adaptor related protein complex 4 subunit beta 1 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

1p13.2

Genomic location:

Preferred name:

NM_001253852.3(AP4B1):c.618-13G>C

HGVS:

NC_000001.11:g.113900413C>G
NG_031901.1:g.9707G>C
NG_057565.1:g.795C>G
NM_001253852.3:c.618-13G>CMANE SELECT
NM_001253853.3:c.321-13G>C
NM_001308312.2:c.114-13G>C
NM_006594.5:c.618-13G>C
LRG_1219:g.795C>G
NC_000001.10:g.114443035C>G
NM_006594.2:c.618-13G>C
NM_006594.3:c.618-13G>C
NR_037864.1:n.910C>G
NR_125965.1:n.1078C>G

Links:

dbSNP: rs3789613

NCBI 1000 Genomes Browser:

rs3789613

Molecular consequence:

NM_001253852.3:c.618-13G>C - intron variant - [Sequence Ontology: SO:0001627]
NM_001253853.3:c.321-13G>C - intron variant - [Sequence Ontology: SO:0001627]
NM_001308312.2:c.114-13G>C - intron variant - [Sequence Ontology: SO:0001627]
NM_006594.5:c.618-13G>C - intron variant - [Sequence Ontology: SO:0001627]
NR_037864.1:n.910C>G - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_125965.1:n.1078C>G - non-coding transcript variant - [Sequence Ontology: SO:0001619]

Condition(s)

Synonyms:: AllHighlyPenetrant
Identifiers:: MedGen: CN169374

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Chromosome neighbors for GEO Profiles (Select 109133737) (20)
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Chromosome neighbors for GEO Profiles (Select 107271337) (20)
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KIAA1656 [Homo sapiens]
KIAA1656 [Homo sapiens]
Gene ID:85371

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000192060	Genetic Services Laboratory, University of Chicago	criteria provided, single submitter (ACMG Guidelines, 2007)	Likely benign (Dec 13, 2012)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]
SCV000519299	GeneDx	criteria provided, single submitter (GeneDx Variant Classification (06012015))	Benign (Jan 22, 2016)	germline	clinical testing	Citation Link,
SCV001957335	Joint Genome Diagnostic Labs from Nijmegen and Maastricht, Radboudumc and MUMC+ - VKGL Data-share Consensus See additional submitters Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen	no assertion criteria provided	Benign	germline	clinical testing
SCV001978461	Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen - VKGL Data-share Consensus	no assertion criteria provided	Benign	germline	clinical testing

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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	germline	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

ACMG recommendations for standards for interpretation and reporting of sequence variations: Revisions 2007.

Richards CS, Bale S, Bellissimo DB, Das S, Grody WW, Hegde MR, Lyon E, Ward BE; Molecular Subcommittee of the ACMG Laboratory Quality Assurance Committee..

Genet Med. 2008 Apr;10(4):294-300. doi: 10.1097/GIM.0b013e31816b5cae.

PubMed [citation]

PMID:: 18414213

Details of each submission

From Genetic Services Laboratory, University of Chicago, SCV000192060.1

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

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

From GeneDx, SCV000519299.4

#	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 Joint Genome Diagnostic Labs from Nijmegen and Maastricht, Radboudumc and MUMC+ - VKGL Data-share Consensus, SCV001957335.1

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

#	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 Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen - VKGL Data-share Consensus, SCV001978461.1

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

#	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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