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NM_001018115.3(FANCD2):c.1777C>T (p.Pro593Ser) AND Malignant tumor of breast

Germline classification:
Uncertain significance (1 submission)
Last evaluated:
Apr 8, 2020
Review status:
(0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided
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:
RCV001004843.5

Allele description [Variation Report for NM_001018115.3(FANCD2):c.1777C>T (p.Pro593Ser)]

NM_001018115.3(FANCD2):c.1777C>T (p.Pro593Ser)

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.1777C>T (p.Pro593Ser)
HGVS:
  • NC_000003.12:g.10062161C>T
  • NG_007311.1:g.40733C>T
  • NG_046754.1:g.31315C>T
  • NM_001018115.3:c.1777C>TMANE SELECT
  • NM_001319984.2:c.1777C>T
  • NM_001374253.1:c.1666C>T
  • NM_001374254.1:c.1777C>T
  • NM_033084.6:c.1777C>T
  • NP_001018125.1:p.Pro593Ser
  • NP_001018125.1:p.Pro593Ser
  • NP_001306913.1:p.Pro593Ser
  • NP_001361182.1:p.Pro556Ser
  • NP_001361183.1:p.Pro593Ser
  • NP_149075.2:p.Pro593Ser
  • LRG_306t2:c.1777C>T
  • LRG_306:g.40733C>T
  • NC_000003.11:g.10103845C>T
  • NM_001018115.2:c.1777C>T
  • NM_033084.3:c.1777C>T
  • NM_033084.4:c.1777C>T
Protein change:
P556S
Links:
dbSNP: rs147523071
NCBI 1000 Genomes Browser:
rs147523071
Molecular consequence:
  • NM_001018115.3:c.1777C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001319984.2:c.1777C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001374253.1:c.1666C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001374254.1:c.1777C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_033084.6:c.1777C>T - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:
Malignant tumor of breast
Synonyms:
Malignant breast neoplasm; Cancer breast
Identifiers:
MONDO: MONDO:0007254; MedGen: C0006142

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV000987266Center of Medical Genetics and Primary Health Care
no assertion criteria provided
Uncertain significance
(Apr 8, 2020) 		germlineresearch

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineyes1not providednot providednot providednot providedresearch

Details of each submission

From Center of Medical Genetics and Primary Health Care, SCV000987266.2

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
11not providednot providedresearchnot provided

Description

ACMG Guidelines 2015 criteria BS1 Benign Strong: GnomAD exomes allele frequency = 0.000883 > 0.000584 derived from the 206 clinically reported variants in gene FANCD2 of which 16 PATH, 103 VUS and 87 BEN. BP1 Benign Supporting: 32 out of 35 non-VUS missense variants in gene FANCD2 are BEN = 91.4% > threshold of 51.0%, and 87 out of 206 clinically reported variants in gene FANCD2 are BEN = 42.2% > threshold of 24.0%. BP4 Benign Supporting: 13 benign predictions from DANN, DEOGEN2, EIGEN, FATHMM-MKL, M-CAP, MVP, MutationAssessor, MutationTaster, PrimateAI, REVEL, SIFT, PolyPhen-2 and Align-GVGD vs no pathogenic predictions and the position is not conserved. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance.

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

Last Updated: Oct 20, 2024