NC_000003.11:g.(?_9470623)_(11078652_?)dup AND not provided

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Jun 24, 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:: RCV004582249.1

Allele description [Variation Report for NC_000003.11:g.(?_9470623)_(11078652_?)dup]

NC_000003.11:g.(?_9470623)_(11078652_?)dup

Genes:

OGG1:8-oxoguanine DNA glycosylase [Gene - OMIM - HGNC]
ARPC4-TTLL3:ARPC4-TTLL3 readthrough [Gene - HGNC]
ATP2B2:ATPase plasma membrane Ca2+ transporting 2 [Gene - OMIM - HGNC]
BRK1:BRICK1 subunit of SCAR/WAVE actin nucleating complex [Gene - OMIM - HGNC]
EMC3:ER membrane protein complex subunit 3 [Gene - OMIM - HGNC]
FANCD2:FA complementation group D2 [Gene - OMIM - HGNC]
FANCD2OS:FANCD2 opposite strand [Gene - HGNC]
LHFPL4:LHFPL tetraspan subfamily member 4 [Gene - OMIM - HGNC]
RPUSD3:RNA pseudouridine synthase D3 [Gene - OMIM - HGNC]
SEC13:SEC13 homolog, nuclear pore and COPII coat complex component [Gene - OMIM - HGNC]
SETD5:SET domain containing 5 [Gene - OMIM - HGNC]
TATDN2:TatD DNase domain containing 2 [Gene - OMIM - HGNC]
ARPC4:actin related protein 2/3 complex subunit 4 [Gene - OMIM - HGNC]
BRPF1:bromodomain and PHD finger containing 1 [Gene - OMIM - HGNC]
CAMK1:calcium/calmodulin dependent protein kinase I [Gene - OMIM - HGNC]
CIDEC:cell death inducing DFFA like effector c [Gene - OMIM - HGNC]
CPNE9:copine family member 9 [Gene - HGNC]
CRELD1:cysteine rich with EGF like domains 1 [Gene - OMIM - HGNC]
GHRL:ghrelin and obestatin prepropeptide [Gene - OMIM - HGNC]
GHRLOS:ghrelin opposite strand/antisense RNA [Gene - OMIM - HGNC]
IRAK2:interleukin 1 receptor associated kinase 2 [Gene - OMIM - HGNC]
IL17RC:interleukin 17 receptor C [Gene - OMIM - HGNC]
IL17RE:interleukin 17 receptor E [Gene - OMIM - HGNC]
JAGN1:jagunal homolog 1 [Gene - OMIM - HGNC]
MTMR14:myotubularin related protein 14 [Gene - OMIM - HGNC]
PRRT3:proline rich transmembrane protein 3 [Gene - OMIM - HGNC]
SLC6A11:solute carrier family 6 member 11 [Gene - OMIM - HGNC]
SLC6A1:solute carrier family 6 member 1 [Gene - OMIM - HGNC]
TADA3:transcriptional adaptor 3 [Gene - OMIM - HGNC]
TTLL3:tubulin tyrosine ligase like 3 [Gene - OMIM - HGNC]
VHL:von Hippel-Lindau tumor suppressor [Gene - OMIM - HGNC]

Variant type:

Duplication

Cytogenetic location:

3p25.3

Genomic location:

Chr3: 9470623 - 11078652 (on Assembly GRCh37)

Preferred name:

NC_000003.11:g.(?_9470623)_(11078652_?)dup

HGVS:

NC_000003.11:g.(?_9470623)_(11078652_?)dup

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV005066372	Invitae	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Jun 24, 2023)	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

SCV005066372

Invitae

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Jun 24, 2023)

unknown

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	unknown	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 Invitae, SCV005066372.1

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

Description

In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. This variant has not been reported in the literature in individuals affected with SETD5-related conditions. A copy number gain of the genomic region encompassing the full coding sequence of the SETD5 gene has been identified. The boundaries of this event are unknown as they extend beyond the assayed region for this gene and therefore may encompass additional genes. As the precise location of this event is unknown, it may be in tandem or it may be located elsewhere in the genome.

#	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: Jul 7, 2024

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Relating variation to medicine