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NM_000135.4(FANCA):c.4196C>T (p.Ala1399Val) AND Fanconi anemia complementation group A

Germline classification:
Uncertain significance (1 submission)
Last evaluated:
Apr 29, 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:
RCV002282639.1

Allele description [Variation Report for NM_000135.4(FANCA):c.4196C>T (p.Ala1399Val)]

NM_000135.4(FANCA):c.4196C>T (p.Ala1399Val)

Genes:
FANCA:FA complementation group A [Gene - OMIM - HGNC]
ZNF276:zinc finger protein 276 [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
16q24.3
Genomic location:
Preferred name:
NM_000135.4(FANCA):c.4196C>T (p.Ala1399Val)
HGVS:
  • NC_000016.10:g.89738946G>A
  • NG_011706.1:g.82712C>T
  • NM_000135.4:c.4196C>TMANE SELECT
  • NM_001113525.2:c.*700G>AMANE SELECT
  • NM_001286167.3:c.4200C>T
  • NM_152287.4:c.*700G>A
  • NP_000126.2:p.Ala1399Val
  • NP_000126.2:p.Ala1399Val
  • NP_001273096.1:p.Ser1400=
  • LRG_495t1:c.4196C>T
  • LRG_495:g.82712C>T
  • LRG_495p1:p.Ala1399Val
  • NC_000016.9:g.89805354G>A
  • NM_000135.2:c.4196C>T
  • NR_110122.2:n.2700G>A
  • NR_110126.2:n.2583G>A
  • NR_110128.2:n.2523G>A
  • NR_110129.2:n.2617G>A
Protein change:
A1399V
Links:
dbSNP: rs1457671800
NCBI 1000 Genomes Browser:
rs1457671800
Molecular consequence:
  • NM_001113525.2:c.*700G>A - 3 prime UTR variant - [Sequence Ontology: SO:0001624]
  • NM_152287.4:c.*700G>A - 3 prime UTR variant - [Sequence Ontology: SO:0001624]
  • NM_000135.4:c.4196C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NR_110122.2:n.2700G>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_110126.2:n.2583G>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_110128.2:n.2523G>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_110129.2:n.2617G>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NM_001286167.3:c.4200C>T - synonymous variant - [Sequence Ontology: SO:0001819]

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
SCV002570385Johns Hopkins Genomics, Johns Hopkins University
criteria provided, single submitter

(ACMG Guidelines, 2015)		Uncertain significance
(Apr 29, 2022) 		germlineclinical testing

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

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknownnot 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 Johns Hopkins Genomics, Johns Hopkins University, SCV002570385.1

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

Description

This FANCA missense variant (rs1457671800) is rare (<0.1%) in a large population dataset (gnomAD: 1/251486 total alleles; 0.0004%; no homozygotes). This variant has been reported in ClinVar [Variation ID 1399364], but has not been reported in the literature, to our knowledge. Of three bioinformatics tools queried, two predict that the substitution would be damaging while one predicts that it would be tolerated. The alanine residue at this position is evolutionarily conserved across most species assessed. We consider the clinical significance of c.4196C>T to be uncertain at this time.

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

Last Updated: Sep 1, 2024