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NM_000135.4(FANCA):c.2853-2A>C

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Interpretation:
Likely pathogenic​

Review status:
criteria provided, multiple submitters, no conflicts
Submissions:
3 (Most recent: Jan 7, 2021)
Last evaluated:
Sep 9, 2020
Accession:
VCV000557092.5
Variation ID:
557092
Description:
single nucleotide variant
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NM_000135.4(FANCA):c.2853-2A>C

Allele ID
547933
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
16q24.3
Genomic location
16: 89758707 (GRCh38) GRCh38 UCSC
16: 89825115 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
LRG_495t1:c.2853-2A>C
LRG_495:g.62951A>C
NC_000016.10:g.89758707T>G
... more HGVS
Protein change
-
Other names
-
Canonical SPDI
NC_000016.10:89758706:T:G
Functional consequence
-
Global minor allele frequency (GMAF)
-

Allele frequency
The Genome Aggregation Database (gnomAD) 0.00006
Trans-Omics for Precision Medicine (TOPMed) 0.00002
Links
dbSNP: rs947311062
VarSome
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Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Likely pathogenic 2 criteria provided, single submitter Mar 7, 2018 RCV000673183.2
Likely pathogenic 1 criteria provided, single submitter Sep 9, 2020 RCV001240902.2
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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: SCV000798358.1
Submitted: (Jul 10, 2018)
Evidence details
Publications
PubMed (1)
Likely pathogenic
(Sep 09, 2020)
criteria provided, single submitter
Method: clinical testing
Fanconi anemia
Allele origin: germline
Invitae
Accession: SCV001413885.2
Submitted: (Jan 07, 2021)
Evidence details
Publications
PubMed (3)
Comment:
This sequence change affects an acceptor splice site in intron 29 of the FANCA gene. It is expected to disrupt RNA splicing and likely results … (more)
Pathogenic
(Feb 28, 2020)
no assertion criteria provided
Method: curation
Fanconi anemia, complementation group A
Allele origin: germline
Leiden Open Variation Database
Accession: SCV001425702.1
Submitted: (Mar 04, 2020)
Evidence details
Comment:
Curator: Arleen D. Auerbach. Submitter to LOVD: Arleen D. Auerbach.

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
Validation of Fanconi anemia complementation Group A assignment using molecular analysis. Moghrabi NN Genetics in medicine : official journal of the American College of Medical Genetics 2009 PMID: 19367192
Splicing in action: assessing disease causing sequence changes. Baralle D Journal of medical genetics 2005 PMID: 16199547
Spectrum of sequence variations in the FANCA gene: an International Fanconi Anemia Registry (IFAR) study. Levran O Human mutation 2005 PMID: 15643609

Text-mined citations for rs947311062...

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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