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NM_000135.4(FANCA):c.709+5G>A

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Interpretation:
Pathogenic/Likely pathogenic​

Review status:
criteria provided, multiple submitters, no conflicts
Submissions:
6 (Most recent: Jan 7, 2021)
Last evaluated:
Apr 19, 2020
Accession:
VCV000408169.9
Variation ID:
408169
Description:
single nucleotide variant
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NM_000135.4(FANCA):c.709+5G>A

Allele ID
402204
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
16q24.3
Genomic location
16: 89805275 (GRCh38) GRCh38 UCSC
16: 89871683 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
NC_000016.9:g.89871683C>T
NC_000016.10:g.89805275C>T
NG_011706.1:g.16383G>A
... more HGVS
Protein change
-
Other names
IVS7DS, G-A, +5
Canonical SPDI
NC_000016.10:89805274:C:T
Functional consequence
-
Global minor allele frequency (GMAF)
-

Allele frequency
Exome Aggregation Consortium (ExAC) 0.00002
Trans-Omics for Precision Medicine (TOPMed) 0.00001
The Genome Aggregation Database (gnomAD), exomes 0.00002
The Genome Aggregation Database (gnomAD) 0.00003
Links
ClinGen: CA8252848
LOVD 3: FANCA_000046
OMIM: 607139.0012
dbSNP: rs759877008
Varsome
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Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Pathogenic/Likely pathogenic 5 criteria provided, multiple submitters, no conflicts Jan 3, 2020 RCV000673202.5
Pathogenic 1 criteria provided, single submitter Apr 19, 2020 RCV000474895.3
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Gene OMIM ClinGen Gene Dosage Sensitivity Curation Variation viewer Related variants
HI score Help TS score Help Within gene All
FANCA - - GRCh38
GRCh37
2154 2635

Submitted interpretations and evidence

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Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Likely pathogenic
(Mar 07, 2018)
criteria provided, single submitter
Method: clinical testing
Fanconi anemia, complementation group A
Allele origin: unknown
Counsyl
Accession: SCV000798378.1
Submitted: (Jul 10, 2018)
Evidence details
Publications
PubMed (7)
Pathogenic
(Apr 19, 2020)
criteria provided, single submitter
Method: clinical testing
Fanconi anemia
Allele origin: germline
Invitae
Accession: SCV000547740.4
Submitted: (Jan 07, 2021)
Evidence details
Publications
PubMed (6)
Comment:
This variant affects a highly conserved nucleotide within the consensus splice site of intron 7. The majority of introns (75%) have a G at this … (more)
Pathogenic
(Jan 03, 2020)
criteria provided, single submitter
Method: clinical testing
Fanconi anemia, complementation group A
Allele origin: germline
Institute of Human Genetics, University of Leipzig Medical Center
Accession: SCV001429202.1
Submitted: (Apr 20, 2020)
Evidence details
Pathogenic
(Jul 02, 2009)
no assertion criteria provided
Method: literature only
FANCONI ANEMIA, COMPLEMENTATION GROUP A
Allele origin: germline
OMIM
Accession: SCV000224033.3
Submitted: (Jun 22, 2015)
Evidence details
Publications
PubMed (1)
Pathogenic
(Feb 28, 2020)
no assertion criteria provided
Method: curation
Fanconi anemia, complementation group A
Allele origin: germline
Leiden Open Variation Database
Accession: SCV001425625.1
Submitted: (Mar 04, 2020)
Evidence details
Publications
PubMed (3)
Comment:
Curator: Arleen D. Auerbach. Submitters to LOVD: Arleen D. Auerbach, Johan de Winter, Johan den Dunnen.
Pathogenic
(Sep 16, 2020)
no assertion criteria provided
Method: clinical testing
Fanconi anemia, group A
Allele origin: germline
Natera, Inc.
Accession: SCV001459006.1
Submitted: (Dec 28, 2020)
Evidence details

Functional evidence

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There is no functional evidence in ClinVar for this variation. If you have generated functional data for this variation, please consider submitting that data to ClinVar.

Citations for this variant

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Title Author Journal Year Link
A comprehensive approach to identification of pathogenic FANCA variants in Fanconi anemia patients and their families. Kimble DC Human mutation 2018 PMID: 29098742
DNA helicases FANCM and DDX11 are determinants of PARP inhibitor sensitivity. Stoepker C DNA repair 2015 PMID: 25583207
Origin, functional role, and clinical impact of Fanconi anemia FANCA mutations. Castella M Blood 2011 PMID: 21273304
Impaired FANCD2 monoubiquitination and hypersensitivity to camptothecin uniquely characterize Fanconi anemia complementation group M. Singh TR Blood 2009 PMID: 19423727
Genetic subtyping of Fanconi anemia by comprehensive mutation screening. Ameziane N Human mutation 2008 PMID: 17924555
In vitro and in silico analysis reveals an efficient algorithm to predict the splicing consequences of mutations at the 5' splice sites. Sahashi K Nucleic acids research 2007 PMID: 17726045
Aberrant 5' splice sites in human disease genes: mutation pattern, nucleotide structure and comparison of computational tools that predict their utilization. Buratti E Nucleic acids research 2007 PMID: 17576681
Heterogeneous spectrum of mutations in the Fanconi anaemia group A gene. Wijker M European journal of human genetics : EJHG 1999 PMID: 10094191
Statistical features of human exons and their flanking regions. Zhang MQ Human molecular genetics 1998 PMID: 9536098
Expression cloning of a cDNA for the major Fanconi anaemia gene, FAA. Lo Ten Foe JR Nature genetics 1996 PMID: 8896563

Text-mined citations for rs759877008...

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These citations are identified by LitVar using the rs number, so they may include citations for more than one variant at this location. Please review the LitVar results carefully for your variant of interest.

Record last updated Sep 06, 2021