NM_000135.4(FANCA):c.4117A>G (p.Thr1373Ala) AND Fanconi anemia

Germline classification:: Likely benign (2 submissions)
Last evaluated:: Dec 19, 2023
Review status:: 1 star out of maximum of 4 stars
criteria provided, single submitter

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:: RCV001834601.7

Allele description [Variation Report for NM_000135.4(FANCA):c.4117A>G (p.Thr1373Ala)]

NM_000135.4(FANCA):c.4117A>G (p.Thr1373Ala)

Genes:

FANCA:FA complementation group A [Gene - OMIM - HGNC]
ZNF276:zinc finger protein 276 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

16q24.3

Genomic location:

Preferred name:

NM_000135.4(FANCA):c.4117A>G (p.Thr1373Ala)

HGVS:

NC_000016.10:g.89739183T>C
NG_011706.1:g.82475A>G
NM_000135.4:c.4117A>GMANE SELECT
NM_001113525.2:c.*937T>CMANE SELECT
NM_001286167.3:c.4117A>G
NM_152287.4:c.*937T>C
NP_000126.2:p.Thr1373Ala
NP_000126.2:p.Thr1373Ala
NP_001273096.1:p.Thr1373Ala
LRG_495t1:c.4117A>G
LRG_495:g.82475A>G
LRG_495p1:p.Thr1373Ala
NC_000016.9:g.89805591T>C
NM_000135.2:c.4117A>G
NM_000135.3:c.4117A>G
NR_110122.2:n.2937T>C
NR_110126.2:n.2820T>C
NR_110128.2:n.2760T>C
NR_110129.2:n.2854T>C

Protein change:

T1373A

Links:

dbSNP: rs753944130

NCBI 1000 Genomes Browser:

rs753944130

Molecular consequence:

NM_001113525.2:c.*937T>C - 3 prime UTR variant - [Sequence Ontology: SO:0001624]
NM_152287.4:c.*937T>C - 3 prime UTR variant - [Sequence Ontology: SO:0001624]
NM_000135.4:c.4117A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001286167.3:c.4117A>G - missense variant - [Sequence Ontology: SO:0001583]
NR_110122.2:n.2937T>C - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_110126.2:n.2820T>C - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_110128.2:n.2760T>C - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_110129.2:n.2854T>C - non-coding transcript variant - [Sequence Ontology: SO:0001619]

Condition(s)

Name:: Fanconi anemia (FA)
Synonyms:: Fanconi pancytopenia; Fanconi's anemia
Identifiers:: MONDO: MONDO:0019391; MeSH: D005199; MedGen: C0015625; Orphanet: 84; OMIM: PS227650

Recent activity

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zinc transporter ZIP6 isoform 1 precursor [Homo sapiens]
zinc transporter ZIP6 isoform 1 precursor [Homo sapiens]
gi|1519316170|ref|NP_036451.4|

Protein

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV002092474	Natera, Inc.	no assertion criteria provided	Uncertain significance (Oct 28, 2019)	germline	clinical testing
SCV002299008	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Likely benign (Dec 19, 2023)	germline	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

SCV002092474

Natera, Inc.

no assertion criteria provided

Uncertain significance
(Oct 28, 2019)

germline

clinical testing

SCV002299008

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Likely benign
(Dec 19, 2023)

germline

clinical testing

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

Help

Summary from all submissions

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

Citations

PubMed

Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria.

Nykamp K, Anderson M, Powers M, Garcia J, Herrera B, Ho YY, Kobayashi Y, Patil N, Thusberg J, Westbrook M; Invitae Clinical Genomics Group., Topper S.

Genet Med. 2017 Oct;19(10):1105-1117. doi: 10.1038/gim.2017.37. Epub 2017 May 11. Erratum in: Genet Med. 2020 Jan;22(1):240. doi: 10.1038/s41436-019-0624-9.

PubMed [citation]

PMID:: 28492532
PMCID:: PMC5632818

Details of each submission

From Natera, Inc., SCV002092474.1

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

#	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 Labcorp Genetics (formerly Invitae), Labcorp, SCV002299008.3

#	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	germline	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Sep 29, 2024

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