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NM_001018115.3(FANCD2):c.983G>A (p.Arg328Gln)

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Interpretation:
Benign/Likely benign​

Review status:
criteria provided, multiple submitters, no conflicts
Submissions:
9
First in ClinVar:
Jun 9, 2014
Most recent Submission:
Dec 31, 2022
Last evaluated:
May 5, 2022
Accession:
VCV000134310.15
Variation ID:
134310
Description:
single nucleotide variant
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NM_001018115.3(FANCD2):c.983G>A (p.Arg328Gln)

Allele ID
138049
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
3p25.3
Genomic location
3: 10043144 (GRCh38) GRCh38 UCSC
3: 10084828 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
NM_001018115.3:c.983G>A MANE Select NP_001018125.1:p.Arg328Gln missense
NM_001319984.2:c.983G>A NP_001306913.1:p.Arg328Gln missense
NM_001374253.1:c.983G>A NP_001361182.1:p.Arg328Gln missense
... more HGVS
Protein change
R328Q
Other names
-
Canonical SPDI
NC_000003.12:10043143:G:A
Functional consequence
-
Global minor allele frequency (GMAF)
0.00599 (A)

Allele frequency
The Genome Aggregation Database (gnomAD) 0.00089
Trans-Omics for Precision Medicine (TOPMed) 0.00250
Exome Aggregation Consortium (ExAC) 0.00395
Trans-Omics for Precision Medicine (TOPMed) 0.00213
The Genome Aggregation Database (gnomAD), exomes 0.00446
NHLBI Exome Sequencing Project (ESP) Exome Variant Server 0.00023
The Genome Aggregation Database (gnomAD) 0.00124
1000 Genomes Project 0.00599
Links
ClinGen: CA159423
UniProtKB: Q9BXW9#VAR_025832
dbSNP: rs35625434
VarSome
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Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Benign/Likely benign 4 criteria provided, multiple submitters, no conflicts Dec 10, 2021 RCV000120984.6
Benign 2 criteria provided, multiple submitters, no conflicts Dec 17, 2021 RCV001084208.6
Benign/Likely benign 2 criteria provided, multiple submitters, no conflicts May 5, 2022 RCV001146799.4
Likely benign 1 criteria provided, single submitter Oct 3, 2016 RCV000443739.5
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Gene OMIM ClinGen Gene Dosage Sensitivity Curation Variation viewer Related variants
HI score Help TS score Help Within gene All
FANCD2 - - GRCh38
GRCh37
51 1042
LOC107303338 - - - GRCh38 - 669

Submitted interpretations and evidence

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Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter More information
Benign
(Jan 13, 2018)
criteria provided, single submitter
Method: clinical testing
Fanconi anemia complementation group D2
Affected status: unknown
Allele origin: germline
Illumina Laboratory Services,Illumina
Accession: SCV001307558.1
First in ClinVar: May 31, 2020
Last updated: May 31, 2020
Comment:
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 … (more)
Benign
(Jun 10, 2020)
criteria provided, single submitter
Method: clinical testing
not specified
Affected status: no
Allele origin: germline
Genetic Services Laboratory,University of Chicago
Accession: SCV002070976.1
First in ClinVar: Jan 29, 2022
Last updated: Jan 29, 2022
Benign
(Dec 17, 2021)
criteria provided, single submitter
Method: clinical testing
Fanconi anemia
Affected status: unknown
Allele origin: germline
Invitae
Accession: SCV000291164.7
First in ClinVar: Jul 01, 2016
Last updated: May 16, 2022
Likely benign
(May 05, 2022)
criteria provided, single submitter
Method: clinical testing
Fanconi anemia complementation group D2
Affected status: unknown
Allele origin: unknown
Fulgent Genetics, Fulgent Genetics
Accession: SCV002799447.1
First in ClinVar: Dec 31, 2022
Last updated: Dec 31, 2022
Likely Benign
(Oct 03, 2016)
criteria provided, single submitter
Method: clinical testing
not provided
Affected status: not provided
Allele origin: germline
Center for Pediatric Genomic Medicine,Children's Mercy Hospital and Clinics
Accession: SCV000511359.1
First in ClinVar: Mar 08, 2017
Last updated: Mar 08, 2017
Comment:
Converted during submission to Likely benign.
Likely benign
(Dec 10, 2021)
criteria provided, single submitter
Method: clinical testing
not specified
Affected status: unknown
Allele origin: germline
Women's Health and Genetics/Laboratory Corporation of America, LabCorp
Accession: SCV002051021.1
First in ClinVar: Jan 08, 2022
Last updated: Jan 08, 2022
Benign
(May 06, 2021)
criteria provided, single submitter
Method: curation
Fanconi anemia
Affected status: unknown
Allele origin: germline
Sema4,Sema4
Accession: SCV002529542.1
First in ClinVar: Jun 24, 2022
Last updated: Jun 24, 2022
Benign
(-)
no assertion criteria provided
Method: clinical testing
not specified
Affected status: yes
Allele origin: unknown
Department of Pathology and Laboratory Medicine,Sinai Health System
Additional submitter:
Franklin by Genoox
Study: The Canadian Open Genetics Repository (COGR)
Accession: SCV001550817.1
First in ClinVar: Apr 13, 2021
Last updated: Apr 13, 2021
Comment:
The FANCD2 p.Arg328Gln variant was identified in 1 of 48 proband chromosomes (frequency: 0.021) from individuals with Fanconi anemia (Nie_2019). The p.R328Q variant was identified … (more)
not provided
(Sep 19, 2013)
no assertion provided
Method: reference population
AllHighlyPenetrant
Affected status: unknown
Allele origin: germline
ITMI
Accession: SCV000085152.1
First in ClinVar: Jun 09, 2014
Last updated: Jun 09, 2014
Comment:
Please see associated publication for description of ethnicities
Publications:
PubMed (1)
PubMed: 24728327

Observation 1:

Ethnicity/Population group: Whole_cohort

Observation 2:

Ethnicity/Population group: African

Observation 3:

Ethnicity/Population group: African_European

Observation 4:

Ethnicity/Population group: Central_Asian

Observation 5:

Ethnicity/Population group: East_Asian

Observation 6:

Ethnicity/Population group: European

Observation 7:

Ethnicity/Population group: Hispanic

Functional evidence

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There is no functional evidence in ClinVar for this variation. If you have generated functional data for this variation, please consider submitting that data to ClinVar.

Citations for this variant

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Title Author Journal Year Link
Germline variation in cancer-susceptibility genes in a healthy, ancestrally diverse cohort: implications for individual genome sequencing. Bodian DL PloS one 2014 PMID: 24728327

Text-mined citations for rs35625434...

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These citations are identified by LitVar using the rs number, so they may include citations for more than one variant at this location. Please review the LitVar results carefully for your variant of interest.

Record last updated Jan 07, 2023