NM_000135.4(FANCA):c.3008A>G (p.Asn1003Ser) AND Fanconi anemia complementation group A

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Oct 11, 2022
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:: RCV003154060.1

Allele description [Variation Report for NM_000135.4(FANCA):c.3008A>G (p.Asn1003Ser)]

NM_000135.4(FANCA):c.3008A>G (p.Asn1003Ser)

Gene:

FANCA:FA complementation group A [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

16q24.3

Genomic location:

Preferred name:

NM_000135.4(FANCA):c.3008A>G (p.Asn1003Ser)

HGVS:

NC_000016.10:g.89752196T>C
NG_011706.1:g.69462A>G
NM_000135.2:c.3008A>G
NM_000135.4:c.3008A>GMANE SELECT
NM_001286167.3:c.3008A>G
NP_000126.2:p.Asn1003Ser
NP_001273096.1:p.Asn1003Ser
LRG_495t1:c.3008A>G
LRG_495:g.69462A>G
NC_000016.9:g.89818604T>C

Protein change:

N1003S

Links:

dbSNP: rs757175768

NCBI 1000 Genomes Browser:

rs757175768

Molecular consequence:

NM_000135.4:c.3008A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001286167.3:c.3008A>G - missense variant - [Sequence Ontology: SO:0001583]

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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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV003843085	St. Jude Molecular Pathology, St. Jude Children's Research Hospital	criteria provided, single submitter (St. Jude Assertion Criteria 2020)	Uncertain significance (Oct 11, 2022)	germline	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV003843085

St. Jude Molecular Pathology, St. Jude Children's Research Hospital

criteria provided, single submitter

(St. Jude Assertion Criteria 2020)

Uncertain significance
(Oct 11, 2022)

germline

clinical testing

Citation Link

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

Details of each submission

From St. Jude Molecular Pathology, St. Jude Children's Research Hospital, SCV003843085.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	not provided

Description

The FANCA c.3008A>G (p.Asn1003Ser) missense change has a maximum subpopulation frequency of 0.056% in gnomAD v2.1.1 (https://gnomad.broadinstitute.org/). The in silico tool REVEL predicts a benign effect on protein function, but to our knowledge this prediction has not been confirmed by functional studies. To our knowledge, this variant has not been reported in individuals with Fanconi anemia. In summary, the evidence currently available is insufficient to determine the clinical significance of this variant. It has therefore been classified as of uncertain significance.

#	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: Feb 20, 2024

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