NM_032444.4(SLX4):c.2975G>A (p.Gly992Glu) AND Fanconi anemia

Germline classification:: Conflicting interpretations of pathogenicity (2 submissions)
Last evaluated:: Jan 18, 2024
Review status:: criteria provided, conflicting classifications

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:: RCV000351349.16

Allele description [Variation Report for NM_032444.4(SLX4):c.2975G>A (p.Gly992Glu)]

NM_032444.4(SLX4):c.2975G>A (p.Gly992Glu)

Gene:

SLX4:SLX4 structure-specific endonuclease subunit [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

16p13.3

Genomic location:

Preferred name:

NM_032444.4(SLX4):c.2975G>A (p.Gly992Glu)

HGVS:

NC_000016.10:g.3590663C>T
NG_028123.1:g.25922G>A
NM_032444.4:c.2975G>AMANE SELECT
NP_115820.2:p.Gly992Glu
LRG_503t1:c.2975G>A
LRG_503:g.25922G>A
NC_000016.9:g.3640664C>T
NM_032444.2:c.2975G>A
NM_032444.3:c.2975G>A

Protein change:

G992E

Links:

dbSNP: rs139287784

NCBI 1000 Genomes Browser:

rs139287784

Molecular consequence:

NM_032444.4:c.2975G>A - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

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

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000547444	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Benign (Jan 18, 2024)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]
SCV002529316	Sema4, Sema4	criteria provided, single submitter (Sema4 Curation Guidelines)	Uncertain significance (Nov 29, 2021)	germline	curation	PubMed (6) [See all records that cite these PMIDs] 29891941, 22383991, 23211700, 32546565, 30268473, 23840564 Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000547444

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Benign
(Jan 18, 2024)

germline

clinical testing

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

SCV002529316

Sema4, Sema4

criteria provided, single submitter

(Sema4 Curation Guidelines)

Uncertain significance
(Nov 29, 2021)

germline

curation

PubMed (6)
[See all records that cite these PMIDs]

Citation Link

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, curation

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

Rare variants in Fanconi anemia genes are enriched in acute myeloid leukemia.

Maung KZY, Leo PJ, Bassal M, Casolari DA, Gray JX, Bray SC, Pederson S, Singhal D, Samaraweera SE, Nguyen T, Cildir G, Marshall M, Ewing A, Duncan EL, Brown MA, Saal R, Tergaonkar V, To LB, Marlton P, Gill D, Lewis I, Deans AJ, et al.

Blood Cancer J. 2018 Jun 1;8(6):50. doi: 10.1038/s41408-018-0090-7. No abstract available.

PubMed [citation]

PMID:: 29891941
PMCID:: PMC6002376

See all PubMed Citations (7)

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV000547444.9

#	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

From Sema4, Sema4, SCV002529316.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	curation	PubMed (6)

#	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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