NC_000001.10:g.(?_206941981)_(208391267_?)dup AND Inflammatory bowel disease

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Mar 25, 2021
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:: RCV001916125.4

Allele description [Variation Report for NC_000001.10:g.(?_206941981)_(208391267_?)dup]

NC_000001.10:g.(?_206941981)_(208391267_?)dup

Genes:

PFKFB2:6-phosphofructo-2-kinase/fructose-2,6-biphosphatase 2 [Gene - OMIM - HGNC]
CD34:CD34 molecule [Gene - OMIM - HGNC]
CD46:CD46 molecule [Gene - OMIM - HGNC]
CD55:CD55 molecule (Cromer blood group) [Gene - OMIM - HGNC]
FCAMR:Fc alpha and mu receptor [Gene - OMIM - HGNC]
FCMR:Fc mu receptor [Gene - OMIM - HGNC]
MIR29B2CHG:MIR29B2 and MIR29C host gene [Gene - HGNC]
YOD1:YOD1 deubiquitinase [Gene - OMIM - HGNC]
C1orf116:chromosome 1 open reading frame 116 [Gene - OMIM - HGNC]
CR1:complement C3b/C4b receptor 1 (Knops blood group) [Gene - OMIM - HGNC]
CR1L:complement C3b/C4b receptor 1 like [Gene - OMIM - HGNC]
CR2:complement C3d receptor 2 [Gene - OMIM - HGNC]
C4BPA:complement component 4 binding protein alpha [Gene - OMIM - HGNC]
C4BPB:complement component 4 binding protein beta [Gene - OMIM - HGNC]
IL10:interleukin 10 [Gene - OMIM - HGNC]
IL19:interleukin 19 [Gene - OMIM - HGNC]
IL20:interleukin 20 [Gene - OMIM - HGNC]
IL24:interleukin 24 [Gene - OMIM - HGNC]
MIR29C:microRNA 29c [Gene - OMIM - HGNC]
PLXNA2:plexin A2 [Gene - OMIM - HGNC]
PIGR:polymeric immunoglobulin receptor [Gene - OMIM - HGNC]

Variant type:

Duplication

Cytogenetic location:

1q32.1-32.2

Genomic location:

Chr1: 206941981 - 208391267 (on Assembly GRCh37)

Preferred name:

NC_000001.10:g.(?_206941981)_(208391267_?)dup

HGVS:

NC_000001.10:g.(?_206941981)_(208391267_?)dup

Condition(s)

Name:: Inflammatory bowel disease
Identifiers:: MONDO: MONDO:0005265; MedGen: C0021390; OMIM: PS266600

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV002182470	Invitae	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Mar 25, 2021)	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

SCV002182470

Invitae

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Mar 25, 2021)

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):240-242.

PubMed [citation]

PMID:: 28492532
PMCID:: PMC5632818

Details of each submission

From Invitae, SCV002182470.3

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

Description

A copy number gain of the genomic region encompassing the full coding sequence of the IL10 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. This variant has not been reported in the literature in individuals with IL10-related conditions. Experimental studies and prediction algorithms are not available or were not evaluated, and the functional significance of this variant is currently unknown. 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.

#	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: Nov 11, 2023

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