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NM_001018115.3(FANCD2):c.983G>A (p.Arg328Gln) AND Fanconi anemia complementation group D2

Clinical significance:Benign/Likely benign (Last evaluated: May 5, 2022)

Review status:2 stars out of maximum of 4 stars

criteria provided, multiple submitters, no conflicts

Based on:
2 submissions [Details]
Record status:
current
Accession:
RCV001146799.4

Allele description [Variation Report for NM_001018115.3(FANCD2):c.983G>A (p.Arg328Gln)]

NM_001018115.3(FANCD2):c.983G>A (p.Arg328Gln)

Genes:
LOC107303338:3p25 FANCD2 Alu-mediated recombination region [Gene]
FANCD2:FA complementation group D2 [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
3p25.3
Genomic location:
Preferred name:
NM_001018115.3(FANCD2):c.983G>A (p.Arg328Gln)
HGVS:
  • NC_000003.12:g.10043144G>A
  • NG_007311.1:g.21716G>A
  • NG_046754.1:g.12298G>A
  • NM_001018115.3:c.983G>AMANE SELECT
  • NM_001319984.2:c.983G>A
  • NM_001374253.1:c.983G>A
  • NM_001374254.1:c.983G>A
  • NM_033084.6:c.983G>A
  • NP_001018125.1:p.Arg328Gln
  • NP_001306913.1:p.Arg328Gln
  • NP_001361182.1:p.Arg328Gln
  • NP_001361183.1:p.Arg328Gln
  • NP_149075.2:p.Arg328Gln
  • LRG_306t2:c.983G>A
  • LRG_306:g.21716G>A
  • NC_000003.11:g.10084828G>A
  • NM_033084.3:c.983G>A
  • NM_033084.4:c.983G>A
  • Q9BXW9:p.Arg328Gln
Protein change:
R328Q
Links:
UniProtKB: Q9BXW9#VAR_025832; dbSNP: rs35625434
NCBI 1000 Genomes Browser:
rs35625434
Molecular consequence:
  • NM_001018115.3:c.983G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001319984.2:c.983G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001374253.1:c.983G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001374254.1:c.983G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_033084.6:c.983G>A - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:
Fanconi anemia complementation group D2
Synonyms:
FANCONI PANCYTOPENIA, TYPE 4; FANCONI ANEMIA, COMPLEMENTATION GROUP D
Identifiers:
MONDO: MONDO:0009214; MedGen: C3160738; Orphanet: 84; OMIM: 227646

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV001307558Illumina Laboratory Services,Illuminacriteria provided, single submitter
Benign
(Jan 13, 2018)
germlineclinical testing

Citation Link,

SCV002799447Fulgent Genetics, Fulgent Geneticscriteria provided, single submitter
Likely benign
(May 5, 2022)
unknownclinical testing

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

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical testing
not providedunknownunknownnot providednot 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 Illumina Laboratory Services,Illumina, SCV001307558.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testingnot provided

Description

This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

From Fulgent Genetics, Fulgent Genetics, SCV002799447.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (1)
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1unknownunknownnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Jan 7, 2023

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