NM_001195248.2(APTX):c.484-12_484-11insG AND not provided

Germline classification:: Benign (3 submissions)
Last evaluated:: Jan 22, 2024
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:: RCV001672727.17

Allele description [Variation Report for NM_001195248.2(APTX):c.484-12_484-11insG]

NM_001195248.2(APTX):c.484-12_484-11insG

Gene:

APTX:aprataxin [Gene - OMIM - HGNC]

Variant type:

Insertion

Cytogenetic location:

9p21.1

Genomic location:

Preferred name:

NM_001195248.2(APTX):c.484-12_484-11insG

HGVS:

NC_000009.12:g.32986041_32986042insC
NG_012821.2:g.44090_44091insG
NM_001195248.2:c.484-12_484-11insGMANE SELECT
NM_001195249.2:c.484-12_484-11insG
NM_001195250.2:c.322-12_322-11insG
NM_001195251.2:c.484-12_484-11insG
NM_001195252.2:c.268-12_268-11insG
NM_001195254.2:c.322-12_322-11insG
NM_001368995.1:c.484-12_484-11insG
NM_001368996.1:c.484-12_484-11insG
NM_001368997.1:c.484-12_484-11insG
NM_001368998.1:c.484-12_484-11insG
NM_001368999.1:c.484-12_484-11insG
NM_001369000.1:c.322-12_322-11insG
NM_001369001.1:c.322-12_322-11insG
NM_001369002.1:c.220-12_220-11insG
NM_001369003.1:c.220-12_220-11insG
NM_001369004.1:c.220-12_220-11insG
NM_001369005.1:c.220-12_220-11insG
NM_001369006.1:c.220-12_220-11insG
NM_001370669.1:c.220-12_220-11insG
NM_001370670.1:c.220-12_220-11insG
NM_001370673.1:c.220-12_220-11insG
NM_175069.3:c.484-12_484-11insG
NM_175073.3:c.484-12_484-11insG
NC_000009.11:g.32986039_32986040insC
NM_175073.2:c.484-12_484-11insG

Links:

dbSNP: rs377129152

NCBI 1000 Genomes Browser:

rs377129152

Molecular consequence:

NM_001195248.2:c.484-12_484-11insG - intron variant - [Sequence Ontology: SO:0001627]
NM_001195249.2:c.484-12_484-11insG - intron variant - [Sequence Ontology: SO:0001627]
NM_001195250.2:c.322-12_322-11insG - intron variant - [Sequence Ontology: SO:0001627]
NM_001195251.2:c.484-12_484-11insG - intron variant - [Sequence Ontology: SO:0001627]
NM_001195252.2:c.268-12_268-11insG - intron variant - [Sequence Ontology: SO:0001627]
NM_001195254.2:c.322-12_322-11insG - intron variant - [Sequence Ontology: SO:0001627]
NM_001368995.1:c.484-12_484-11insG - intron variant - [Sequence Ontology: SO:0001627]
NM_001368996.1:c.484-12_484-11insG - intron variant - [Sequence Ontology: SO:0001627]
NM_001368997.1:c.484-12_484-11insG - intron variant - [Sequence Ontology: SO:0001627]
NM_001368998.1:c.484-12_484-11insG - intron variant - [Sequence Ontology: SO:0001627]
NM_001368999.1:c.484-12_484-11insG - intron variant - [Sequence Ontology: SO:0001627]
NM_001369000.1:c.322-12_322-11insG - intron variant - [Sequence Ontology: SO:0001627]
NM_001369001.1:c.322-12_322-11insG - intron variant - [Sequence Ontology: SO:0001627]
NM_001369002.1:c.220-12_220-11insG - intron variant - [Sequence Ontology: SO:0001627]
NM_001369003.1:c.220-12_220-11insG - intron variant - [Sequence Ontology: SO:0001627]
NM_001369004.1:c.220-12_220-11insG - intron variant - [Sequence Ontology: SO:0001627]
NM_001369005.1:c.220-12_220-11insG - intron variant - [Sequence Ontology: SO:0001627]
NM_001369006.1:c.220-12_220-11insG - intron variant - [Sequence Ontology: SO:0001627]
NM_001370669.1:c.220-12_220-11insG - intron variant - [Sequence Ontology: SO:0001627]
NM_001370670.1:c.220-12_220-11insG - intron variant - [Sequence Ontology: SO:0001627]
NM_001370673.1:c.220-12_220-11insG - intron variant - [Sequence Ontology: SO:0001627]
NM_175069.3:c.484-12_484-11insG - intron variant - [Sequence Ontology: SO:0001627]
NM_175073.3:c.484-12_484-11insG - intron variant - [Sequence Ontology: SO:0001627]

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV001882756	GeneDx	criteria provided, single submitter (GeneDx Variant Classification Process June 2021)	Benign (Aug 6, 2019)	germline	clinical testing	Citation Link,
SCV001922442	Clinical Genetics, Academic Medical Center - VKGL Data-share Consensus See additional submitters Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen	no assertion criteria provided	Likely benign	germline	clinical testing
SCV002378094	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Benign (Jan 22, 2024)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV001882756

GeneDx

criteria provided, single submitter

(GeneDx Variant Classification Process June 2021)

Benign
(Aug 6, 2019)

germline

clinical testing

Citation Link,

SCV001922442

Clinical Genetics, Academic Medical Center - VKGL Data-share Consensus

See additional submitters

no assertion criteria provided

Likely benign

germline

clinical testing

SCV002378094

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Benign
(Jan 22, 2024)

germline

clinical testing

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

Citations

PubMed

Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria.

Nykamp K, Anderson M, Powers M, Garcia J, Herrera B, Ho YY, Kobayashi Y, Patil N, Thusberg J, Westbrook M; Invitae Clinical Genomics Group, Topper S.

Genet Med. 2017 Oct;19(10):1105-1117. doi: 10.1038/gim.2017.37. Epub 2017 May 11. Erratum in: Genet Med. 2020 Jan;22(1):240. doi: 10.1038/s41436-019-0624-9.

PubMed [citation]

PMID:: 28492532
PMCID:: PMC5632818

Details of each submission

From GeneDx, SCV001882756.1

#	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 Clinical Genetics, Academic Medical Center - VKGL Data-share Consensus, SCV001922442.1

#	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 Labcorp Genetics (formerly Invitae), Labcorp, SCV002378094.3

#	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

Last Updated: Nov 24, 2024

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