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NM_000135.4(FANCA):c.2317-30_2317-1del AND Fanconi anemia complementation group A

Germline classification:
Pathogenic (1 submission)
Review status:
1 star out of maximum of 4 stars
criteria provided, single submitter
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:
RCV004557282.2

Allele description [Variation Report for NM_000135.4(FANCA):c.2317-30_2317-1del]

NM_000135.4(FANCA):c.2317-30_2317-1del

Gene:
FANCA:FA complementation group A [Gene - OMIM - HGNC]
Variant type:
Deletion
Cytogenetic location:
16q24.3
Genomic location:
Preferred name:
NM_000135.4(FANCA):c.2317-30_2317-1del
HGVS:
  • NC_000016.10:g.89770029_89770058del
  • NG_011706.1:g.51604_51633del
  • NM_000135.4:c.2317-30_2317-1delMANE SELECT
  • NM_001286167.3:c.2317-30_2317-1del
  • LRG_495:g.51604_51633del
  • NC_000016.9:g.89836437_89836466del
Links:
dbSNP: rs2544196390
NCBI 1000 Genomes Browser:
rs2544196390
Molecular consequence:
  • NM_000135.4:c.2317-30_2317-1del - splice acceptor variant - [Sequence Ontology: SO:0001574]
  • NM_001286167.3:c.2317-30_2317-1del - splice acceptor variant - [Sequence Ontology: SO:0001574]
Observations:
1

Condition(s)

Name:
Fanconi anemia complementation group A
Synonyms:
Fanconi anemia, group A
Identifiers:
MONDO: MONDO:0009215; MedGen: C3469521; Orphanet: 84; OMIM: 227650

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV005046463HUSP Clinical Genetics Laboratory, Hospital Universitario San Pedro De Logroño (HUSP)
criteria provided, single submitter

(ACMG Guidelines, 2015)		Pathogenicunknownclinical testing

PubMed (1)
[See all records that cite this PMID]

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedunknownyes1not providednot providednot providednot providedclinical testing

Citations

PubMed

Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology.

Richards S, Aziz N, Bale S, Bick D, Das S, Gastier-Foster J, Grody WW, Hegde M, Lyon E, Spector E, Voelkerding K, Rehm HL; ACMG Laboratory Quality Assurance Committee.

Genet Med. 2015 May;17(5):405-24. doi: 10.1038/gim.2015.30. Epub 2015 Mar 5.

PubMed [citation]
PMID:
25741868
PMCID:
PMC4544753

Details of each submission

From HUSP Clinical Genetics Laboratory, Hospital Universitario San Pedro De Logroño (HUSP), SCV005046463.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not provided1not providednot providedclinical testing PubMed (1)

Description

The variant was detected in a 6-years old boy with clinic related to Fanconi anemia (pancytopenia, hearing loss, abnormal ear morphology, thumb deformity, cafe-au-lait spots). He presented two heterozygous variants in FANCA, c.3066+1G>A and c.2317-30_2317-1del (NM_000135.4). The variant c.2317-30_2317-1del is found in the last 30 nucleotides of 25 intron, which results in a canonical splicing donor modification, changing the conventional splicing process. This variant is not detected in general population and has not been reported in pathogenic data bases. Pathogenic variants in FANCA have been associated with Fanconi anemia (OMIM: 607139).This clinical entity is characterized by bone marrow failure, abnormal skin pigmentation, skeletal malformations, microcephaly, ophthalmological disorders, genitourinary tract anomalies and susceptibility to cancer. This entity has autosomal recessive inheritance.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1unknownyesnot providednot providednot provided1not providednot providednot provided

Last Updated: May 16, 2025