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NM_032193.4(RNASEH2C):c.417C>G (p.Gly139=) AND Aicardi-Goutieres syndrome 3

Clinical significance:Conflicting interpretations of pathogenicity, Uncertain significance(1); Benign(1); Likely benign(1) (Last evaluated: Dec 17, 2021)

Review status:1 star out of maximum of 4 stars

criteria provided, conflicting interpretations

Based on:
4 submissions [Details]
Record status:
current
Accession:
RCV000557783.13

Allele description [Variation Report for NM_032193.4(RNASEH2C):c.417C>G (p.Gly139=)]

NM_032193.4(RNASEH2C):c.417C>G (p.Gly139=)

Gene:
RNASEH2C:ribonuclease H2 subunit C [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
11q13.1
Genomic location:
Preferred name:
NM_032193.4(RNASEH2C):c.417C>G (p.Gly139=)
HGVS:
  • NC_000011.10:g.65720096G>C
  • NG_008976.2:g.5843C>G
  • NG_033057.1:g.13095G>C
  • NM_032193.4:c.417C>GMANE SELECT
  • NP_115569.2:p.Gly139=
  • NP_115569.2:p.Gly139=
  • LRG_280t1:c.417C>G
  • LRG_280:g.5843C>G
  • LRG_280p1:p.Gly139=
  • NC_000011.9:g.65487567G>C
  • NM_032193.3:c.417C>G
Links:
dbSNP: rs147021687
NCBI 1000 Genomes Browser:
rs147021687
Molecular consequence:
  • NM_032193.4:c.417C>G - synonymous variant - [Sequence Ontology: SO:0001819]

Condition(s)

Name:
Aicardi-Goutieres syndrome 3
Identifiers:
MONDO: MONDO:0012471; MedGen: C1835916; Orphanet: 51; OMIM: 610329

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV000373158Illumina Laboratory Services,Illuminacriteria provided, single submitter
Uncertain significance
(Jan 13, 2018)
germlineclinical testing

Citation Link,

SCV000638653Invitaecriteria provided, single submitter
Benign
(Dec 17, 2021)
germlineclinical testing

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

SCV000733082Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen - VKGL Data-share Consensusno assertion criteria providedLikely benigngermlineclinical testing

SCV000744889Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center - VKGL Data-share Consensuscriteria provided, single submitter
Likely benign
(Jun 28, 2017)
germlineclinical testing

Citation Link

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineyesnot providednot providednot providednot providednot providedclinical testing
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical 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 Illumina Laboratory Services,Illumina, SCV000373158.3

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testingnot provided

Description

This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score, this variant could not be ruled out of causing disease and therefore its association with disease required further investigation. A literature search was performed for the gene, cDNA change, and amino acid change (if applicable). No publications were found based on this search. This variant was therefore classified as a variant of unknown significance for this disease.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

From Invitae, SCV000638653.5

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (1)
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

From Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen - VKGL Data-share Consensus, SCV000733082.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testingnot provided
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineyesnot providednot providednot providednot providednot providednot providednot provided

From Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center - VKGL Data-share Consensus, SCV000744889.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testingnot provided
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineyesnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Aug 23, 2022

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