NM_032444.4(SLX4):c.86G>A (p.Arg29His) AND Fanconi anemia

Germline classification:: Benign/Likely benign (2 submissions)
Last evaluated:: Dec 12, 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:: RCV000473920.12

Allele description [Variation Report for NM_032444.4(SLX4):c.86G>A (p.Arg29His)]

NM_032444.4(SLX4):c.86G>A (p.Arg29His)

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.86G>A (p.Arg29His)

HGVS:

NC_000016.10:g.3608879C>T
NG_028123.1:g.7706G>A
NM_032444.3:c.86G>A
NM_032444.4:c.86G>AMANE SELECT
NP_115820.2:p.Arg29His
LRG_503t1:c.86G>A
LRG_503:g.7706G>A
NC_000016.9:g.3658880C>T
NM_032444.2:c.86G>A

Protein change:

R29H

Links:

dbSNP: rs149117119

NCBI 1000 Genomes Browser:

rs149117119

Molecular consequence:

NM_032444.4:c.86G>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

Recent activity

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Chromosome neighbors for GEO Profiles (Select 115985024) (20)
GEO Profiles
Homo sapiens isolate CHM13 chromosome 4, alternate assembly T2T-CHM13v2.0
Homo sapiens isolate CHM13 chromosome 4, alternate assembly T2T-CHM13v2.0
gi|2194974292|gnl|ASM:GCF_009914825 f|NC_060928.1||gpp|GPC_000012743.1||gnl|NCBI_GENOMES|119564

Nucleotide
Homo sapiens chromosome 19 open reading frame 41, mRNA (cDNA clone IMAGE:5298058...
Homo sapiens chromosome 19 open reading frame 41, mRNA (cDNA clone IMAGE:5298058), partial cds
gi|20809876|gb|BC029535.1|

Nucleotide

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000547451	Invitae	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Benign (Dec 12, 2023)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]
SCV002529399	Sema4, Sema4	criteria provided, single submitter (Sema4 Curation Guidelines)	Likely benign (Jun 3, 2021)	germline	curation	PubMed (1) [See all records that cite this PMID] Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000547451

Invitae

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Benign
(Dec 12, 2023)

germline

clinical testing

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

SCV002529399

Sema4, Sema4

criteria provided, single submitter

(Sema4 Curation Guidelines)

Likely benign
(Jun 3, 2021)

germline

curation

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

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

Population-based targeted sequencing of 54 candidate genes identifies PALB2 as a susceptibility gene for high-grade serous ovarian cancer.

Song H, Dicks EM, Tyrer J, Intermaggio M, Chenevix-Trench G, Bowtell DD, Traficante N, Group A, Brenton J, Goranova T, Hosking K, Piskorz A, van Oudenhove E, Doherty J, Harris HR, Rossing MA, Duerst M, Dork T, Bogdanova NV, Modugno F, Moysich K, Odunsi K, et al.

J Med Genet. 2021 May;58(5):305-313. doi: 10.1136/jmedgenet-2019-106739. Epub 2020 Jun 16.

PubMed [citation]

PMID:: 32546565
PMCID:: PMC8086250

Details of each submission

From Invitae, SCV000547451.9

#	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, SCV002529399.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	curation	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: Feb 28, 2024

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