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NM_004629.2(FANCG):c.890C>T (p.Thr297Ile) AND Fanconi anemia complementation group G

Germline classification:
Benign (4 submissions)
Last evaluated:
Jul 7, 2023
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:
RCV001166139.7

Allele description [Variation Report for NM_004629.2(FANCG):c.890C>T (p.Thr297Ile)]

NM_004629.2(FANCG):c.890C>T (p.Thr297Ile)

Genes:
VCP:valosin containing protein [Gene - OMIM - HGNC]
FANCG:FA complementation group G [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
9p13.3
Genomic location:
Preferred name:
NM_004629.2(FANCG):c.890C>T (p.Thr297Ile)
HGVS:
  • NC_000009.12:g.35076758G>A
  • NG_007312.1:g.8259C>T
  • NG_007887.1:g.985C>T
  • NM_004629.2:c.890C>TMANE SELECT
  • NP_004620.1:p.Thr297Ile
  • NP_004620.1:p.Thr297Ile
  • LRG_499t1:c.890C>T
  • LRG_499:g.8259C>T
  • LRG_499p1:p.Thr297Ile
  • LRG_657:g.985C>T
  • NC_000009.11:g.35076755G>A
  • NM_004629.1:c.890C>T
  • O15287:p.Thr297Ile
Protein change:
T297I
Links:
UniProtKB: O15287#VAR_020311; dbSNP: rs2237857
NCBI 1000 Genomes Browser:
rs2237857
Molecular consequence:
  • NM_004629.2:c.890C>T - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:
Fanconi anemia complementation group G
Synonyms:
Fanconi anemia group G
Identifiers:
MONDO: MONDO:0013565; MedGen: C3469527; Orphanet: 84; OMIM: 614082

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV001328479Illumina Laboratory Services, Illumina
criteria provided, single submitter

(ICSL Variant Classification Criteria 13 December 2019)
Benign
(Mar 6, 2018)
germlineclinical testing

Citation Link,

SCV001364822Leiden Open Variation Database
no assertion criteria provided
Pathogenic
(Feb 7, 2011)
germlinecuration

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

SCV001452305Natera, Inc.
no assertion criteria provided
Benign
(Sep 16, 2020)
germlineclinical testing

SCV004017689KCCC/NGS Laboratory, Kuwait Cancer Control Center
criteria provided, single submitter

(ACMG Guidelines, 2015)
Benign
(Jul 7, 2023)
germlineclinical testing

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

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical testing
not providedgermlineyesnot providednot providednot providednot providednot providedclinical testing, curation

Citations

PubMed

Functional analysis of patient-derived mutations in the Fanconi anemia gene, FANCG/XRCC9.

Nakanishi K, Moran A, Hays T, Kuang Y, Fox E, Garneau D, Montes de Oca R, Grompe M, D'Andrea AD.

Exp Hematol. 2001 Jul;29(7):842-9.

PubMed [citation]
PMID:
11438206

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 Illumina Laboratory Services, Illumina, SCV001328479.1

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

Description

This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease.

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

From Leiden Open Variation Database, SCV001364822.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedcuration PubMed (1)

Description

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

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

From Natera, Inc., SCV001452305.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testingnot provided
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

From KCCC/NGS Laboratory, Kuwait Cancer Control Center, SCV004017689.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (1)
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineyesnot providednot providednot providednot providednot providednot providednot provided

Last Updated: May 19, 2024