NC_000016.9:g.(?_89871693)_(89878808_?)del AND Fanconi anemia

This record was updated by the submitter. Please see the current version.

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Mar 24, 2019
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:: RCV004581538.1

Allele description

NC_000016.9:g.(?_89871693)_(89878808_?)del

Gene:: FANCA:FA complementation group A [Gene - OMIM - HGNC]
Variant type:: Deletion
Cytogenetic location:: 16q24.3
Genomic location:: Chr16: 89871693 - 89878808 (on Assembly GRCh37)
Preferred name:: NC_000016.9:g.(?_89871693)_(89878808_?)del
HGVS:: NC_000016.9:g.(?_89871693)_(89878808_?)del
This HGVS expression did not pass validation

Condition(s)

Name:: Fanconi anemia (FA)
Synonyms:: Fanconi pancytopenia; Fanconi's anemia
Identifiers:: MONDO: MONDO:0019391; MeSH: D005199; MedGen: C0015625; Orphanet: 84; OMIM: PS227650

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV005066866	Invitae	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Pathogenic (Mar 24, 2019)	unknown	clinical testing	PubMed (2) [See all records that cite these PMIDs] 19367192, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV005066866

Invitae

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Pathogenic
(Mar 24, 2019)

unknown

clinical testing

PubMed (2)
[See all records that cite these PMIDs]

Help

Summary from all submissions

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

Citations

PubMed

Validation of Fanconi anemia complementation Group A assignment using molecular analysis.

Moghrabi NN, Johnson MA, Yoshitomi MJ, Zhu X, Al-Dhalimy MJ, Olson SB, Grompe M, Richards CS.

Genet Med. 2009 Mar;11(3):183-92. doi: 10.1097/GIM.0b013e318193ba67.

PubMed [citation]

PMID:: 19367192

Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria.

Nykamp K, Anderson M, Powers M, Garcia J, Herrera B, Ho YY, Kobayashi Y, Patil N, Thusberg J, Westbrook M; Invitae Clinical Genomics Group., Topper S.

Genet Med. 2017 Oct;19(10):1105-1117. doi: 10.1038/gim.2017.37. Epub 2017 May 11. Erratum in: Genet Med. 2020 Jan;22(1):240. doi: 10.1038/s41436-019-0624-9.

PubMed [citation]

PMID:: 28492532
PMCID:: PMC5632818

Details of each submission

From Invitae, SCV005066866.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (2)

Description

For these reasons, this variant has been classified as Pathogenic. Loss-of-function variants in FANCA are known to be pathogenic (PMID: 19367192). Similar deletions described as deletion of exons 4-7 have been observed in individuals with clinical features of Fanconi anemia (PMID:¬†29098742, 26799702, Invitae). This variant is a deletion of the genomic region encompassing exons 4-6 and part of exon 7 (c.284-1329_704del) of the FANCA gene. It is expected to disrupt RNA splicing and likely results in an absent or disrupted protein product.

#	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: Jul 7, 2024

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