NM_002184.4(IL6ST):c.2702T>G (p.Met901Arg) AND not provided

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Jul 18, 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:: RCV003565781.3

Allele description [Variation Report for NM_002184.4(IL6ST):c.2702T>G (p.Met901Arg)]

NM_002184.4(IL6ST):c.2702T>G (p.Met901Arg)

Gene:

IL6ST:interleukin 6 cytokine family signal transducer [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

5q11.2

Genomic location:

Preferred name:

NM_002184.4(IL6ST):c.2702T>G (p.Met901Arg)

HGVS:

NC_000005.10:g.55941137A>C
NM_001190981.2:c.2519T>G
NM_001364275.2:c.2600T>G
NM_001364276.2:c.2492T>G
NM_001364277.2:c.1835T>G
NM_001364278.2:c.1799T>G
NM_001364279.2:c.1706T>G
NM_002184.4:c.2702T>GMANE SELECT
NM_175767.3:c.*1629T>G
NP_001177910.1:p.Met840Arg
NP_001351204.1:p.Met867Arg
NP_001351205.1:p.Met831Arg
NP_001351206.1:p.Met612Arg
NP_001351207.1:p.Met600Arg
NP_001351208.1:p.Met569Arg
NP_002175.2:p.Met901Arg
NC_000005.9:g.55236965A>C
NR_120480.2:n.3031T>G
NR_157112.2:n.3866T>G

Protein change:

M569R

Molecular consequence:

NM_175767.3:c.*1629T>G - 3 prime UTR variant - [Sequence Ontology: SO:0001624]
NM_001190981.2:c.2519T>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001364275.2:c.2600T>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001364276.2:c.2492T>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001364277.2:c.1835T>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001364278.2:c.1799T>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001364279.2:c.1706T>G - missense variant - [Sequence Ontology: SO:0001583]
NM_002184.4:c.2702T>G - missense variant - [Sequence Ontology: SO:0001583]
NR_120480.2:n.3031T>G - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_157112.2:n.3866T>G - non-coding transcript variant - [Sequence Ontology: SO:0001619]

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
SCV004309140	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Jul 18, 2023)	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

SCV004309140

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Jul 18, 2023)

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, SCV004309140.1

#	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. An algorithm developed to predict the effect of missense changes on protein structure and function (PolyPhen-2) suggests that this variant¬†is likely to be tolerated. This variant has not been reported in the literature in individuals affected with IL6ST-related conditions. This variant is not present in population databases (gnomAD no frequency). This sequence change replaces methionine, which is neutral and non-polar, with arginine, which is basic and polar, at codon 901 of the IL6ST protein (p.Met901Arg).

#	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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