NM_001018115.3(FANCD2):c.983G>A (p.Arg328Gln) AND Fanconi anemia complementation group D2

Clinical significance:Benign/Likely benign (Last evaluated: May 5, 2022)
Review status:2 stars out of maximum of 4 stars
criteria provided, multiple submitters, no conflicts

Based on:: 2 submissions [Details]
Record status:: current
Accession:: RCV001146799.4

Allele description [Variation Report for NM_001018115.3(FANCD2):c.983G>A (p.Arg328Gln)]

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

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.983G>A (p.Arg328Gln)

HGVS:

NC_000003.12:g.10043144G>A
NG_007311.1:g.21716G>A
NG_046754.1:g.12298G>A
NM_001018115.3:c.983G>AMANE SELECT
NM_001319984.2:c.983G>A
NM_001374253.1:c.983G>A
NM_001374254.1:c.983G>A
NM_033084.6:c.983G>A
NP_001018125.1:p.Arg328Gln
NP_001306913.1:p.Arg328Gln
NP_001361182.1:p.Arg328Gln
NP_001361183.1:p.Arg328Gln
NP_149075.2:p.Arg328Gln
LRG_306t2:c.983G>A
LRG_306:g.21716G>A
NC_000003.11:g.10084828G>A
NM_033084.3:c.983G>A
NM_033084.4:c.983G>A
Q9BXW9:p.Arg328Gln

Protein change:

R328Q

Links:

UniProtKB: Q9BXW9#VAR_025832; dbSNP: rs35625434

NCBI 1000 Genomes Browser:

rs35625434

Molecular consequence:

NM_001018115.3:c.983G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001319984.2:c.983G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001374253.1:c.983G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001374254.1:c.983G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_033084.6:c.983G>A - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:: Fanconi anemia complementation group D2
Synonyms:: FANCONI PANCYTOPENIA, TYPE 4; FANCONI ANEMIA, COMPLEMENTATION GROUP D
Identifiers:: MONDO: MONDO:0009214; MedGen: C3160738; Orphanet: 84; OMIM: 227646

Recent activity

Clear Turn Off Turn On

Your browsing activity is empty.

Activity recording is turned off.

Turn recording back on

Help

Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV001307558	Illumina Laboratory Services,Illumina	criteria provided, single submitter ICSL Variant Classification Criteria 13 December 2019	Benign (Jan 13, 2018)	germline	clinical testing	Citation Link,
SCV002799447	Fulgent Genetics, Fulgent Genetics	criteria provided, single submitter ACMG Guidelines, 2015	Likely benign (May 5, 2022)	unknown	clinical testing	PubMed (1) [See all records that cite this PMID]

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV001307558

Illumina Laboratory Services,Illumina

criteria provided, single submitter

ICSL Variant Classification Criteria 13 December 2019

Benign
(Jan 13, 2018)

germline

clinical testing

Citation Link,

SCV002799447

Fulgent Genetics, Fulgent Genetics

criteria provided, single submitter

ACMG Guidelines, 2015

Likely benign
(May 5, 2022)

unknown

clinical testing

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

Summary from all submissions

Help

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

Citations

PubMed

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, SCV001307558.1

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

#	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 Fulgent Genetics, Fulgent Genetics, SCV002799447.1

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

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

Last Updated: Jan 7, 2023

ClinVar

Relating variation to medicine