NM_000136.3(FANCC):c.816C>T (p.Ile272=) AND not provided

Germline classification:: Benign (3 submissions)
Last evaluated:: Mar 1, 2024
Review status:: 2 stars out of maximum of 4 stars
criteria provided, multiple submitters, no conflicts

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:: RCV000588252.15

Allele description [Variation Report for NM_000136.3(FANCC):c.816C>T (p.Ile272=)]

NM_000136.3(FANCC):c.816C>T (p.Ile272=)

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.816C>T (p.Ile272=)

Other names:

p.I272I:ATC>ATT

HGVS:

NC_000009.12:g.95135373G>A
NG_011707.1:g.187337C>T
NM_000136.3:c.816C>TMANE SELECT
NM_001243743.2:c.816C>T
NM_001243744.2:c.816C>T
NP_000127.2:p.Ile272=
NP_001230672.1:p.Ile272=
NP_001230673.1:p.Ile272=
LRG_497t1:c.816C>T
LRG_497:g.187337C>T
NC_000009.11:g.97897655G>A
NM_000136.2:c.816C>T

Links:

dbSNP: rs55719336

NCBI 1000 Genomes Browser:

rs55719336

Molecular consequence:

NM_000136.3:c.816C>T - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001243743.2:c.816C>T - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001243744.2:c.816C>T - synonymous variant - [Sequence Ontology: SO:0001819]

Observations:

Condition(s)

Synonyms:: none provided; RECLASSIFIED - ADRA2C POLYMORPHISM; RECLASSIFIED - ADRB1 POLYMORPHISM
Identifiers:: MedGen: C3661900

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000695438	Women's Health and Genetics/Laboratory Corporation of America, LabCorp	criteria provided, single submitter (LabCorp Variant Classification Summary - May 2015)	Benign (Apr 29, 2016)	germline	clinical testing	LabCorp Variant Classification Summary - May 2015.docx, Citation Link,
SCV001365323	Leiden Open Variation Database	no assertion criteria provided	Uncertain significance (Feb 28, 2020)	germline	curation	PubMed (1) [See all records that cite this PMID]
SCV004811157	CeGaT Center for Human Genetics Tuebingen	criteria provided, single submitter (CeGaT Center For Human Genetics Tuebingen Variant Classification Criteria Version 2)	Benign (Mar 1, 2024)	germline	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000695438

Women's Health and Genetics/Laboratory Corporation of America, LabCorp

criteria provided, single submitter

(LabCorp Variant Classification Summary - May 2015)

Benign
(Apr 29, 2016)

germline

clinical testing

LabCorp Variant Classification Summary - May 2015.docx,

Citation Link,

SCV001365323

Leiden Open Variation Database

no assertion criteria provided

Uncertain significance
(Feb 28, 2020)

germline

curation

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

SCV004811157

CeGaT Center for Human Genetics Tuebingen

criteria provided, single submitter

(CeGaT Center For Human Genetics Tuebingen Variant Classification Criteria Version 2)

Benign
(Mar 1, 2024)

germline

clinical testing

Citation Link

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	yes	1	not provided	not provided	not provided	not provided	clinical testing, curation
not provided	germline	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

Evaluation of Fanconi Anemia genes in familial breast cancer predisposition.

Seal S, Barfoot R, Jayatilake H, Smith P, Renwick A, Bascombe L, McGuffog L, Evans DG, Eccles D, Easton DF, Stratton MR, Rahman N; Breast Cancer Susceptibility Collaboration.

Cancer Res. 2003 Dec 15;63(24):8596-9.

PubMed [citation]

PMID:: 14695169

Details of each submission

From Women's Health and Genetics/Laboratory Corporation of America, LabCorp, SCV000695438.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	not provided

Description

Variant summary: The FANCC c.816C>T (p.Ile272Ile) variant affects a non-conserved nucleotide, resulting in a synonymous mutation. Mutation taster predicts damaging outcome for this variant while 5/5 in silico tools via Alamut predict the variant not to have an impact on normal splicing. The variant was observed by the ExAC project in 159/121094 control chromosomes (1 homozygote) at a frequency of 0.001313, which does not exceed maximal expected frequency of a pathogenic allele (0.0017678). However, in the East Asian subcohort, the variant was observed at an allele frequency of 0.015 which exceeds the estimated maximal expected allele frequency of a disease causing FANCC allele indicating the variant to be a neutral polymorphism in populations of East Asian origin. In addition, two independent clinical laboratory databases classified this variant as Benign via ClinVar (without evidence to independently evaluate). Considering the high prevalence of the variant in the East Asian population, it was classified as Benign.

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

From Leiden Open Variation Database, SCV001365323.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	curation	PubMed (1)

Description

Curator: Arleen D. Auerbach. Submitter to LOVD: Arleen D. Auerbach.

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	yes	not provided	not provided	not provided		not provided	not provided	not provided	not provided

From CeGaT Center for Human Genetics Tuebingen, SCV004811157.10

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	1	not provided	not provided	clinical testing	not provided

Description

FANCC: BP4, BP7, BS1, BS2

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	yes	not provided	not provided	not provided		1	not provided	not provided	not provided

Last Updated: Apr 20, 2025

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