NM_000135.4(FANCA):c.2602-13CT[2] AND not provided

Clinical significance:Conflicting interpretations of pathogenicity, Likely pathogenic(1); Uncertain significance(2) (Last evaluated: Jun 8, 2022)
Review status:1 star out of maximum of 4 stars
criteria provided, conflicting interpretations

Help

Based on:: 3 submissions [Details]
Record status:: current
Accession:: RCV000858161.16

Allele description [Variation Report for NM_000135.4(FANCA):c.2602-13CT[2]]

NM_000135.4(FANCA):c.2602-13CT[2]

Gene:

FANCA:FA complementation group A [Gene - OMIM - HGNC]

Variant type:

Microsatellite

Cytogenetic location:

16q24.3

Genomic location:

Preferred name:

NM_000135.4(FANCA):c.2602-13CT[2]

HGVS:

NC_000016.10:g.89765074AG[2]
NG_011706.1:g.56579CT[2]
NM_000135.4:c.2602-13CT[2]MANE SELECT
NM_001286167.3:c.2602-13CT[2]
LRG_495t1:c.2602-9_2602-8del
LRG_495:g.56579CT[2]
NC_000016.9:g.89831482AG[2]
NC_000016.9:g.89831482_89831483del
NM_000135.2:c.2602-9_2602-8del
NM_000135.2:c.2602-9_2602-8delCT
NM_000135.3:c.2602-9_2602-8del
NM_000135.4:c.2602-9_2602-8delCTMANE SELECT

Links:

dbSNP: rs577636020

NCBI 1000 Genomes Browser:

rs577636020

Molecular consequence:

NM_000135.4:c.2602-13CT[2] - intron variant - [Sequence Ontology: SO:0001627]
NM_001286167.3:c.2602-13CT[2] - intron variant - [Sequence Ontology: SO:0001627]

Observations:

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: CN517202

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV001151105	CeGaT Center for Human Genetics Tuebingen	criteria provided, single submitter Praxis fuer Humangenetik Tuebingen - Variant Classification Criteria	Likely pathogenic (Feb 1, 2019)	germline	clinical testing	Citation Link,
SCV001764073	GeneDx	criteria provided, single submitter GeneDx Variant Classification Process June 2021	Uncertain significance (Mar 5, 2020)	germline	clinical testing	Citation Link,
SCV002047088	Quest Diagnostics Nichols Institute San Juan Capistrano	criteria provided, single submitter Quest Diagnostics criteria	Uncertain significance (Jun 8, 2022)	unknown	clinical testing	PubMed (4) [See all records that cite these PMIDs] 32235514, 30306255, 29098742, 26467025

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV001151105

CeGaT Center for Human Genetics Tuebingen

criteria provided, single submitter

Praxis fuer Humangenetik Tuebingen - Variant Classification Criteria

Likely pathogenic
(Feb 1, 2019)

germline

clinical testing

Citation Link,

SCV001764073

GeneDx

criteria provided, single submitter

GeneDx Variant Classification Process June 2021

Uncertain significance
(Mar 5, 2020)

germline

clinical testing

Citation Link,

SCV002047088

Quest Diagnostics Nichols Institute San Juan Capistrano

criteria provided, single submitter

Quest Diagnostics criteria

Uncertain significance
(Jun 8, 2022)

unknown

clinical testing

PubMed (4)
[See all records that cite these PMIDs]

Summary from all submissions

Help

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	unknown	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing
not provided	germline	yes	1	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

Exploring the Role of Mutations in Fanconi Anemia Genes in Hereditary Cancer Patients.

Del Valle J, Rofes P, Moreno-Cabrera JM, López-Dóriga A, Belhadj S, Vargas-Parra G, Teulé À, Cuesta R, Muñoz X, Campos O, Salinas M, de Cid R, Brunet J, González S, Capellá G, Pineda M, Feliubadaló L, Lázaro C.

Cancers (Basel). 2020 Mar 30;12(4). doi:pii: E829. 10.3390/cancers12040829.

PubMed [citation]

PMID:: 32235514
PMCID:: PMC7226125

Multigene panel testing beyond BRCA1/2 in breast/ovarian cancer Spanish families and clinical actionability of findings.

Bonache S, Esteban I, Moles-Fernández A, Tenés A, Duran-Lozano L, Montalban G, Bach V, Carrasco E, Gadea N, López-Fernández A, Torres-Esquius S, Mancuso F, Caratú G, Vivancos A, Tuset N, Balmaña J, Gutiérrez-Enríquez S, Diez O.

J Cancer Res Clin Oncol. 2018 Dec;144(12):2495-2513. doi: 10.1007/s00432-018-2763-9. Epub 2018 Oct 10.

PubMed [citation]

PMID:: 30306255

See all PubMed Citations (4)

Details of each submission

From CeGaT Center for Human Genetics Tuebingen, SCV001151105.14

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

From GeneDx, SCV001764073.1

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

Description

Variant detected in two families with Fanconi Anemia and was shown to lead to aberrant splicing by RT-PCR (Kimble 2018); In-silico analysis, which includes splice predictors and evolutionary conservation, is inconclusive as to whether the variant alters gene splicing.; This variant is associated with the following publications: (PMID: 32235514, 29098742, 25589003)

#	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 Quest Diagnostics Nichols Institute San Juan Capistrano, SCV002047088.2

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (4)

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

Last Updated: Jan 21, 2023

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