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NM_001113378.2(FANCI):c.3865A>G (p.Ile1289Val) AND not specified

Germline classification:
Benign (1 submission)
Last evaluated:
Dec 12, 2019
Review status:
1 star out of maximum of 4 stars
criteria provided, single submitter
Somatic classification
of clinical impact:
Review status:
(0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided
Somatic classification
of oncogenicity:
Review status:
(0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided
Record status:

Allele description [Variation Report for NM_001113378.2(FANCI):c.3865A>G (p.Ile1289Val)]

NM_001113378.2(FANCI):c.3865A>G (p.Ile1289Val)

FANCI:FA complementation group I [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
Genomic location:
Preferred name:
NM_001113378.2(FANCI):c.3865A>G (p.Ile1289Val)
  • NC_000015.10:g.89315330A>G
  • NG_008218.2:g.24466T>C
  • NG_011736.1:g.76368A>G
  • NM_001113378.2:c.3865A>GMANE SELECT
  • NM_001376910.1:c.3586A>G
  • NM_001376911.1:c.3865A>G
  • NM_018193.3:c.3685A>G
  • NP_001106849.1:p.Ile1289Val
  • NP_001106849.1:p.Ile1289Val
  • NP_001363839.1:p.Ile1196Val
  • NP_001363840.1:p.Ile1289Val
  • NP_060663.2:p.Ile1229Val
  • LRG_500t1:c.3865A>G
  • LRG_500:g.76368A>G
  • LRG_500p1:p.Ile1289Val
  • LRG_765:g.24466T>C
  • NC_000015.9:g.89858561A>G
  • NM_001113378.1:c.3865A>G
Protein change:
dbSNP: rs114549781
NCBI 1000 Genomes Browser:
Molecular consequence:
  • NM_001113378.2:c.3865A>G - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001376910.1:c.3586A>G - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001376911.1:c.3865A>G - missense variant - [Sequence Ontology: SO:0001583]
  • NM_018193.3:c.3685A>G - missense variant - [Sequence Ontology: SO:0001583]


MedGen: CN169374

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
SCV001363470Women's Health and Genetics/Laboratory Corporation of America, LabCorp
criteria provided, single submitter

(LabCorp Variant Classification Summary - May 2015)
(Dec 12, 2019)
germlineclinical testing

Citation Link

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical testing

Details of each submission

From Women's Health and Genetics/Laboratory Corporation of America, LabCorp, SCV001363470.1

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


Variant summary: FANCI c.3865A>G (p.Ile1289Val) results in a conservative amino acid change located in the FANCI solenoid 4 domain (IPR029314) of the encoded protein sequence. Four of five in-silico tools predict a damaging effect of the variant on protein function. The variant allele was found at a frequency of 0.00035 in 251470 control chromosomes, predominantly at a frequency of 0.004 within the African or African-American subpopulation in the gnomAD database, including 1 homozygote. The observed variant frequency within African or African-American control individuals in the gnomAD database is approximately 14 fold of the estimated maximal expected allele frequency for a pathogenic variant in FANCI causing Fanconi anemia phenotype (0.00028), strongly suggesting that the variant is a benign polymorphism found primarily in populations of African or African-American origin. To our knowledge, no occurrence of c.3865A>G in individuals affected with Fanconi anemia, complementation group I and no experimental evidence demonstrating its impact on protein function have been reported. One ClinVar submitter (evaluation after 2014) cites the variant as benign. Based on the evidence outlined above, the variant was classified as benign.

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

Last Updated: Jul 15, 2024