NM_000135.4(FANCA):c.306del (p.Ser103fs) AND Fanconi anemia

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Oct 28, 2023
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:: RCV003779025.2

Allele description [Variation Report for NM_000135.4(FANCA):c.306del (p.Ser103fs)]

NM_000135.4(FANCA):c.306del (p.Ser103fs)

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.306del (p.Ser103fs)

HGVS:

NC_000016.10:g.89811050del
NG_011706.1:g.10609del
NM_000135.4:c.306delMANE SELECT
NM_001018112.3:c.306del
NM_001286167.3:c.306del
NM_001351830.2:c.306del
NP_000126.2:p.Ser103Glnfs
NP_000126.2:p.Ser103fs
NP_001018122.1:p.Ser103fs
NP_001273096.1:p.Ser103fs
NP_001338759.1:p.Ser103fs
LRG_495t1:c.305del
LRG_495:g.10609del
LRG_495p1:p.Ser103Glnfs
NC_000016.9:g.89877457del
NC_000016.9:g.89877458del
NM_000135.2:c.305delC

Protein change:

S103fs

Molecular consequence:

NM_000135.4:c.306del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001018112.3:c.306del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001286167.3:c.306del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001351830.2:c.306del - frameshift variant - [Sequence Ontology: SO:0001589]

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
SCV004681380	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Pathogenic (Oct 28, 2023)	germline	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

SCV004681380

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Pathogenic
(Oct 28, 2023)

germline

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	germline	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 Labcorp Genetics (formerly Invitae), Labcorp, SCV004681380.1

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

Description

This sequence change creates a premature translational stop signal (p.Ser103Glnfs*35) in the FANCA gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in FANCA are known to be pathogenic (PMID: 19367192). This variant is not present in population databases (gnomAD no frequency). This variant has not been reported in the literature in individuals affected with FANCA-related conditions. For these reasons, this variant has been classified as Pathogenic.

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Sep 29, 2024

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