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NM_000136.3(FANCC):c.686+5G>A AND Fanconi anemia complementation group C

Germline classification:
Likely pathogenic (1 submission)
Last evaluated:
Jan 13, 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:
RCV004554786.1

Allele description [Variation Report for NM_000136.3(FANCC):c.686+5G>A]

NM_000136.3(FANCC):c.686+5G>A

Genes:
FANCC:FA complementation group C [Gene - OMIM - HGNC]
AOPEP:aminopeptidase O (putative) [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
9q22.32
Genomic location:
Preferred name:
NM_000136.3(FANCC):c.686+5G>A
HGVS:
  • NC_000009.12:g.95149918C>T
  • NG_011707.1:g.172792G>A
  • NM_000136.3:c.686+5G>AMANE SELECT
  • NM_001243743.2:c.686+5G>A
  • NM_001243744.2:c.686+5G>A
  • LRG_497t1:c.686+5G>A
  • LRG_497:g.172792G>A
  • NC_000009.11:g.97912200C>T
  • NM_000136.2:c.686+5G>A
Links:
dbSNP: rs1064794691
NCBI 1000 Genomes Browser:
rs1064794691
Molecular consequence:
  • NM_000136.3:c.686+5G>A - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001243743.2:c.686+5G>A - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001243744.2:c.686+5G>A - intron variant - [Sequence Ontology: SO:0001627]
Observations:
1

Condition(s)

Name:
Fanconi anemia complementation group C (FANCC)
Synonyms:
FANCONI PANCYTOPENIA, TYPE 3; FACC; Fanconi anemia, group C
Identifiers:
MONDO: MONDO:0009213; MedGen: C3468041; Orphanet: 84; OMIM: 227645

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Assertion and evidence details

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Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV005044140New York Genome Center - PrenatalSEQ
criteria provided, single submitter

(NYGC Assertion Criteria 2020)		Likely pathogenic
(Jan 13, 2023) 		inheritedclinical testing

Citation Link

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Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedinheritedyes1not providednot provided1not providedclinical testing

Details of each submission

From New York Genome Center - PrenatalSEQ, SCV005044140.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not provided1not providednot providedclinical testingnot provided

Description

The c.686+5G>A variant in FANCC has not previously been reported in the literature and is deposited in ClinVar [ClinVar ID: 420766] as a Variant of Uncertain Significance. The c.686+5G>A variant is absent from population databases (gnomAD v2.1.1 and v3.1.2, TOPMed Freeze 8), suggesting it is not a common benign variant in the populations represented in those databases. The c.686+5G>A variant is located in the splice region after exon 7 of this 15-exon gene and is predicted to affect mRNA splicing (Splice AI = 0.7287) however, there are no functional studies to support or refute this prediction. Based on available evidence, this inherited c.686+5G>A variant identified in FANCC is classified as Likely pathogenic.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1inheritedyes1not providednot provided1not providednot providednot provided

Last Updated: Oct 8, 2024