ClinVar Genomic variation as it relates to human health
NM_000135.4(FANCA):c.709+5G>A
The aggregate germline classification for this variant, typically for a monogenic or Mendelian disorder as in the ACMG/AMP guidelines, or for response to a drug. This value is calculated by NCBI based on data from submitters. Read our rules for calculating the aggregate classification.
Stars represent the aggregate review status, or the level of review supporting the aggregate germline classification for this VCV record. This value is calculated by NCBI based on data from submitters. Read our rules for calculating the review status. The number of submissions which contribute to this review status is shown in parentheses.
No data submitted for somatic clinical impact
No data submitted for oncogenicity
Variant Details
- Identifiers
-
NM_000135.4(FANCA):c.709+5G>A
Variation ID: 408169 Accession: VCV000408169.24
- Type and length
-
single nucleotide variant, 1 bp
- Location
-
Cytogenetic: 16q24.3 16: 89805275 (GRCh38) [ NCBI UCSC ] 16: 89871683 (GRCh37) [ NCBI UCSC ]
- Timeline in ClinVar
-
First in ClinVar Help The date this variant first appeared in ClinVar with each type of classification.
Last submission Help The date of the most recent submission for each type of classification for this variant.
Last evaluated Help The most recent date that a submitter evaluated this variant for each type of classification.
Germline Apr 17, 2017 Jun 17, 2024 Mar 22, 2024 - HGVS
-
Nucleotide Protein Molecular
consequenceNM_000135.4:c.709+5G>A MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.
intron variant NM_000135.3:c.709+5G>A NM_001018112.3:c.709+5G>A intron variant NM_001286167.3:c.709+5G>A intron variant NM_001351830.2:c.613+5G>A intron variant NC_000016.10:g.89805275C>T NC_000016.9:g.89871683C>T NG_011706.1:g.16383G>A LRG_495:g.16383G>A LRG_495t1:c.709+5G>A - Protein change
- -
- Other names
-
IVS7DS, G-A, +5
- Canonical SPDI
- NC_000016.10:89805274:C:T
-
Functional
consequence HelpThe effect of the variant on RNA or protein function, based on experimental evidence from submitters.
- -
-
Global minor allele
frequency (GMAF) HelpThe global minor allele frequency calculated by the 1000 Genomes Project. The minor allele at this location is indicated in parentheses and may be different from the allele represented by this VCV record.
- -
-
Allele frequency
Help
The frequency of the allele represented by this VCV record.
-
The Genome Aggregation Database (gnomAD), exomes 0.00002
Trans-Omics for Precision Medicine (TOPMed) 0.00002
The Genome Aggregation Database (gnomAD) 0.00001
Exome Aggregation Consortium (ExAC) 0.00002
- Links
Genes
Gene | OMIM | ClinGen Gene Dosage Sensitivity Curation |
Variation Viewer
Help
Links to Variation Viewer, a genome browser to view variation data from NCBI databases. |
Related variants | ||
---|---|---|---|---|---|---|
HI score
Help
The haploinsufficiency score for the gene, curated by ClinGen’s Dosage Sensitivity Curation task team. |
TS score
Help
The triplosensitivity score for the gene, curated by ClinGen’s Dosage Sensitivity Curation task team. |
Within gene
Help
The number of variants in ClinVar that are contained within this gene, with a link to view the list of variants. |
All
Help
The number of variants in ClinVar for this gene, including smaller variants within the gene and larger CNVs that overlap or fully contain the gene. |
|||
FANCA | - | - |
GRCh38 GRCh37 |
4167 | 5325 |
Conditions - Germline
Condition
Help
The condition for this variant-condition (RCV) record in ClinVar. |
Classification
Help
The aggregate germline classification for this variant-condition (RCV) record in ClinVar. The number of submissions that contribute to this aggregate classification is shown in parentheses. (# of submissions) |
Review status
Help
The aggregate review status for this variant-condition (RCV) record in ClinVar. This value is calculated by NCBI based on data from submitters. Read our rules for calculating the review status. |
Last evaluated
Help
The most recent date that a submitter evaluated this variant for the condition. |
Variation/condition record
Help
The RCV accession number, with most recent version number, for the variant-condition record, with a link to the RCV web page. |
---|---|---|---|---|
Pathogenic (1) |
criteria provided, single submitter
|
Dec 12, 2023 | RCV000474895.8 | |
Pathogenic/Likely pathogenic (9) |
criteria provided, multiple submitters, no conflicts
|
Mar 22, 2024 | RCV000673202.14 | |
Pathogenic/Likely pathogenic (2) |
criteria provided, multiple submitters, no conflicts
|
Oct 24, 2022 | RCV001821265.5 |
Submissions - Germline
Classification
Help
The submitted germline classification for each SCV record. (Last evaluated) |
Review status
Help
Stars represent the review status, or the level of review supporting the submitted (SCV) record. This value is calculated by NCBI based on data from the submitter. Read our rules for calculating the review status. This column also includes a link to the submitter’s assertion criteria if provided, and the collection method. (Assertion criteria) |
Condition
Help
The condition for the classification, provided by the submitter for this submitted (SCV) record. This column also includes the affected status and allele origin of individuals observed with this variant. |
Submitter
Help
The submitting organization for this submitted (SCV) record. This column also includes the SCV accession and version number, the date this SCV first appeared in ClinVar, and the date that this SCV was last updated in ClinVar. |
More information
Help
This column includes more information supporting the classification, including citations, the comment on classification, and detailed evidence provided as observations of the variant by the submitter. |
|
---|---|---|---|---|---|
Likely pathogenic
(Mar 07, 2018)
|
criteria provided, single submitter
Method: clinical testing
|
Fanconi anemia complementation group A
Affected status: unknown
Allele origin:
unknown
|
Counsyl
Accession: SCV000798378.1
First in ClinVar: Aug 05, 2018 Last updated: Aug 05, 2018 |
|
|
Pathogenic
(Jan 03, 2020)
|
criteria provided, single submitter
Method: clinical testing
|
Fanconi anemia complementation group A
Affected status: yes
Allele origin:
germline
|
Institute of Human Genetics, University of Leipzig Medical Center
Accession: SCV001429202.1
First in ClinVar: Aug 16, 2020 Last updated: Aug 16, 2020 |
Number of individuals with the variant: 1
|
|
Likely pathogenic
(Dec 14, 2021)
|
criteria provided, single submitter
Method: clinical testing
|
not provided
Affected status: yes
Allele origin:
germline
|
Genetic Services Laboratory, University of Chicago
Accession: SCV002065905.1
First in ClinVar: Jan 29, 2022 Last updated: Jan 29, 2022 |
Comment:
DNA sequence analysis of the FANCA gene demonstrated a sequence change located near the canonical splice donor site in intron 7, c.709+5G>A. This sequence change … (more)
DNA sequence analysis of the FANCA gene demonstrated a sequence change located near the canonical splice donor site in intron 7, c.709+5G>A. This sequence change has been described in the gnomAD database with a frequency of 0.02% in the East Asian subpopulation (dbSNP rs759877008). This sequence change has been previously described, along with other pathogenic variants, in the individuals with Fanconi anemia (PMID: 21273304, 8896563, 19423727, 10094191) and in the heterozygous state in an individual with a personal history of ovarian cancer and family history of Lynch syndrome related cancers (PMID: 32235514). Based on in-silico splice prediction programs, this sequence change likely affects normal splicing of the FANCA gene and an experimental study demonstrated that this sequence change impacts normal splicing leading to the production of an abnormal protein with impaired function (PMID: 19423727). Based on these collective evidences, this sequence change is classified as likely pathogenic. (less)
|
|
Pathogenic
(May 01, 2020)
|
criteria provided, single submitter
Method: clinical testing
|
Fanconi anemia complementation group A
(Autosomal recessive inheritance)
Affected status: yes
Allele origin:
germline
|
Genetics and Molecular Pathology, SA Pathology
Additional submitter:
Shariant Australia, Australian Genomics
Accession: SCV002761920.1
First in ClinVar: Dec 17, 2022 Last updated: Dec 17, 2022 |
Comment:
The FANCA:c.709+5G>A variant is a single base change located in intron 7. The variant has been reported in the literature in individuals with a second … (more)
The FANCA:c.709+5G>A variant is a single base change located in intron 7. The variant has been reported in the literature in individuals with a second pathogenic FANCA variant and is associated with disease (PMID: 21273304, PMID: 29098742) (PS1). RNA studies demonstrate that the variant results in aberrant splicing and the insertion of 30bp intronic sequence. The insertion adds 10 amino acids in-frame between codons 236 and 237 (PMID: 8896563). Functional studies show that the variant is unable to restore FANCD2 monoubiquitination in FANCA-deficient lymphoblasts supporting its pathogenicity (PMID: 19423727) (PS3). The variant is rare in population databases at 0.002% (5 het/ 279588 allele count) (PP). It is described in ClinVar as pathogenic/ likely pathogenic and HGMD (2020.1) as disease causing (PP5). Splice prediction programs in Alamut also predict the variant will remove the exon 7 donor site. (less)
|
|
Pathogenic
(May 06, 2022)
|
criteria provided, single submitter
Method: clinical testing
|
Fanconi anemia complementation group A
Affected status: unknown
Allele origin:
unknown
|
Fulgent Genetics, Fulgent Genetics
Accession: SCV002796743.1
First in ClinVar: Dec 31, 2022 Last updated: Dec 31, 2022 |
|
|
Pathogenic
(Oct 24, 2022)
|
criteria provided, single submitter
Method: clinical testing
|
not provided
Affected status: unknown
Allele origin:
unknown
|
Quest Diagnostics Nichols Institute San Juan Capistrano
Accession: SCV004218640.1
First in ClinVar: Jan 06, 2024 Last updated: Jan 06, 2024 |
Comment:
The frequency of this variant in the general population, 0.0002 (4/19948 chromosomes, http://gnomad.broadinstitute.org), is uninformative in assessment of its pathogenicity. In the published literature, the … (more)
The frequency of this variant in the general population, 0.0002 (4/19948 chromosomes, http://gnomad.broadinstitute.org), is uninformative in assessment of its pathogenicity. In the published literature, the variant has been detected in individuals with Fanconi Anemia. Those individuals were compound heterozygous for the variant and a pathogenic variant in the FANCA gene (PMID: 17924555 (2008), 19423727 (2009), 21273304 (2011), 29098742 (2018)) . It has been reported in an individual with ovarian cancer (PMID: 32235514 (2020)). A functional study has demonstrated that this variant has a deleterious effect on FANCA protein function (PMID: 19423727 (2009)). Analysis of this variant using software algorithms for the prediction of the effect of nucleotide changes on splicing yielded predictions that this variant may affect proper FANCA mRNA splicing . Based on the available information, this variant is classified as pathogenic. (less)
|
|
Pathogenic
(May 10, 2021)
|
criteria provided, single submitter
Method: clinical testing
|
Fanconi anemia complementation group A
Affected status: unknown
Allele origin:
germline
|
Revvity Omics, Revvity
Accession: SCV002022293.3
First in ClinVar: Nov 29, 2021 Last updated: Feb 04, 2024 |
|
|
Pathogenic
(Dec 12, 2023)
|
criteria provided, single submitter
Method: clinical testing
|
Fanconi anemia
Affected status: unknown
Allele origin:
germline
|
Labcorp Genetics (formerly Invitae), Labcorp
Accession: SCV000547740.7
First in ClinVar: Apr 17, 2017 Last updated: Feb 14, 2024 |
Comment:
This sequence change falls in intron 7 of the FANCA gene. It does not directly change the encoded amino acid sequence of the FANCA protein. … (more)
This sequence change falls in intron 7 of the FANCA gene. It does not directly change the encoded amino acid sequence of the FANCA protein. RNA analysis indicates that this variant induces altered splicing and likely results in the gain of 10 novel amino acids amino acid residue(s), but is expected to preserve the integrity of the reading-frame. This variant is present in population databases (rs759877008, gnomAD 0.02%). This variant has been observed in individual(s) with Fanconi anemia (PMID: 8896563, 10094191, 19423727, 21273304). In at least one individual the data is consistent with being in trans (on the opposite chromosome) from a pathogenic variant. This variant is also known as 740+5G>A or IVS7+5G>A. ClinVar contains an entry for this variant (Variation ID: 408169). Algorithms developed to predict the effect of variants on protein structure and function are not available or were not evaluated for this variant. Experimental studies have shown that this variant affects FANCA function (PMID: 19423727). Variants that disrupt the consensus splice site are a relatively common cause of aberrant splicing (PMID: 17576681, 9536098). Studies have shown that this variant results in the activation of a cryptic splice site in intron 7 (PMID: 19423727). For these reasons, this variant has been classified as Pathogenic. (less)
|
|
Pathogenic
(Mar 22, 2024)
|
criteria provided, single submitter
Method: clinical testing
|
Fanconi anemia complementation group A
Affected status: unknown
Allele origin:
unknown
|
Baylor Genetics
Accession: SCV004196024.2
First in ClinVar: Dec 30, 2023 Last updated: Jun 17, 2024 |
|
|
Pathogenic
(Jul 02, 2009)
|
no assertion criteria provided
Method: literature only
|
FANCONI ANEMIA, COMPLEMENTATION GROUP A
Affected status: not provided
Allele origin:
germline
|
OMIM
Accession: SCV000224033.3
First in ClinVar: Jun 28, 2015 Last updated: Feb 17, 2019 |
Comment on evidence:
For discussion of the IVS7+5G-A mutation in the FANCA gene that was found in compound heterozygous state in a patient with Fanconi anemia of complementation … (more)
For discussion of the IVS7+5G-A mutation in the FANCA gene that was found in compound heterozygous state in a patient with Fanconi anemia of complementation group A (FANCA; 227650) by Singh et al. (2009), see 607139.0011. (less)
|
|
Pathogenic
(Feb 28, 2020)
|
no assertion criteria provided
Method: curation
|
Fanconi anemia complementation group A
Affected status: no
Allele origin:
germline
|
Leiden Open Variation Database
Accession: SCV001425625.1
First in ClinVar: Sep 27, 2020 Last updated: Sep 27, 2020 |
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
Affected status: unknown
Allele origin:
germline
|
Natera, Inc.
Accession: SCV001459006.1
First in ClinVar: Jan 02, 2021 Last updated: Jan 02, 2021 |
|
|
click to load more click to collapse |
Germline Functional Evidence
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 germline classification of this variant
HelpTitle | Author | Journal | Year | Link |
---|---|---|---|---|
Exploring the Role of Mutations in Fanconi Anemia Genes in Hereditary Cancer Patients. | Del Valle J | Cancers | 2020 | PMID: 32235514 |
Optimizing clinical exome design and parallel gene-testing for recessive genetic conditions in preconception carrier screening: Translational research genomic data from 14,125 exomes. | Capalbo A | PLoS genetics | 2019 | PMID: 31589614 |
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 |
click to load more click to collapse |
Text-mined citations for rs759877008 ...
HelpRecord last updated Sep 29, 2024
This date represents the last time this VCV record was updated. The update may be due to an update to one of the included submitted records (SCVs), or due to an update that ClinVar made to the variant such as adding HGVS expressions or a rs number. So this date may be different from the date of the “most recent submission” reported at the top of this page.