NM_000572.3(IL10):c.118A>G (p.Met40Val) AND Inflammatory bowel disease

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Jul 21, 2022
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:: RCV003086853.3

Allele description [Variation Report for NM_000572.3(IL10):c.118A>G (p.Met40Val)]

NM_000572.3(IL10):c.118A>G (p.Met40Val)

Genes:

LOC128462409:CRISPRi-FlowFISH-validated IL10 regulatory element GRCh37_chr1:206945468-206946089 [Gene]
IL10:interleukin 10 [Gene - OMIM - HGNC]
IL19:interleukin 19 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

1q32.1

Genomic location:

Preferred name:

NM_000572.3(IL10):c.118A>G (p.Met40Val)

HGVS:

NC_000001.11:g.206772318T>C
NG_012088.1:g.5177A>G
NG_149597.1:g.296T>C
NM_000572.3:c.118A>GMANE SELECT
NM_001393490.1:c.-149+1488T>C
NM_153758.5:c.-149+1240T>CMANE SELECT
NP_000563.1:p.Met40Val
LRG_1230t1:c.118A>G
LRG_1230:g.5177A>G
LRG_1230p1:p.Met40Val
NC_000001.10:g.206945663T>C
NR_168466.1:n.177A>G

Protein change:

M40V

Molecular consequence:

NM_001393490.1:c.-149+1488T>C - intron variant - [Sequence Ontology: SO:0001627]
NM_153758.5:c.-149+1240T>C - intron variant - [Sequence Ontology: SO:0001627]
NM_000572.3:c.118A>G - missense variant - [Sequence Ontology: SO:0001583]
NR_168466.1:n.177A>G - non-coding transcript variant - [Sequence Ontology: SO:0001619]

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
SCV003483071	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Jul 21, 2022)	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

SCV003483071

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Jul 21, 2022)

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 Labcorp Genetics (formerly Invitae), Labcorp, SCV003483071.2

#	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. Algorithms developed to predict the effect of missense changes on protein structure and function are either unavailable or do not agree on the potential impact of this missense change (SIFT: "Tolerated"; PolyPhen-2: "Possibly Damaging"; Align-GVGD: "Class C0"). This variant has not been reported in the literature in individuals affected with IL10-related conditions. This variant is present in population databases (rs755837237, gnomAD 0.05%). This sequence change replaces methionine, which is neutral and non-polar, with valine, which is neutral and non-polar, at codon 40 of the IL10 protein (p.Met40Val).

#	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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