NM_001164508.2(NEB):c.19944G>A (p.Ser6648=) AND not provided

Clinical significance:Conflicting interpretations of pathogenicity, Pathogenic(2);Uncertain significance(1) (Last evaluated: May 15, 2021)

Review status:1 star out of maximum of 4 stars

criteria provided, conflicting interpretations

Based on:
3 submissions [Details]
Record status:
current
Accession:
RCV000224886.6

Allele description [Variation Report for NM_001164508.2(NEB):c.19944G>A (p.Ser6648=)]

NM_001164508.2(NEB):c.19944G>A (p.Ser6648=)

Gene:
NEB:nebulin [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
2q23.3
Genomic location:
Preferred name:
NM_001164508.2(NEB):c.19944G>A (p.Ser6648=)
HGVS:
  • NC_000002.12:g.151551738C>T
  • NG_009382.2:g.187750G>A
  • NM_001164507.2:c.19944G>A
  • NM_001164508.2:c.19944G>AMANE SELECT
  • NM_001271208.2:c.19944G>A
  • NM_004543.5:c.14841G>A
  • NP_001157979.2:p.Ser6648=
  • NP_001157980.2:p.Ser6648=
  • NP_001258137.2:p.Ser6648=
  • NP_004534.3:p.Ser4947=
  • LRG_202t1:c.19944G>A
  • LRG_202:g.187750G>A
  • NC_000002.11:g.152408252C>T
  • NM_001271208.1:c.19944G>A
  • NM_004543.4:c.14841G>A
Links:
dbSNP: rs201553266
NCBI 1000 Genomes Browser:
rs201553266
Molecular consequence:
  • NM_001164507.2:c.19944G>A - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001164508.2:c.19944G>A - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001271208.2:c.19944G>A - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_004543.5:c.14841G>A - synonymous variant - [Sequence Ontology: SO:0001819]
Observations:
1

Condition(s)

Identifiers:
MedGen: CN517202

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV000280967Center for Pediatric Genomic Medicine,Children's Mercy Hospital and Clinicscriteria provided, single submitter
Pathogenic
(Aug 13, 2014)
germlineclinical testing

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

SCV000329870GeneDxcriteria provided, single submitter
Pathogenic
(May 15, 2021)
germlineclinical testing

Citation Link,

SCV000705513EGL Genetic Diagnostics, Eurofins Clinical Diagnosticscriteria provided, single submitter
Uncertain significance
(Feb 24, 2017)
germlineclinical testing

Citation Link

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineyesnot providednot providednot providednot providednot providedclinical testing
not providedgermlinenot providednot providednot providednot providednot providednot providedclinical testing
not providedgermlineunknown1not providednot providednot providednot providedclinical testing

Citations

PubMed

Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology.

Richards S, Aziz N, Bale S, Bick D, Das S, Gastier-Foster J, Grody WW, Hegde M, Lyon E, Spector E, Voelkerding K, Rehm HL; ACMG Laboratory Quality Assurance Committee..

Genet Med. 2015 May;17(5):405-24. doi: 10.1038/gim.2015.30. Epub 2015 Mar 5.

PubMed [citation]
PMID:
25741868
PMCID:
PMC4544753

Details of each submission

From Center for Pediatric Genomic Medicine,Children's Mercy Hospital and Clinics, SCV000280967.2

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (1)
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlinenot providednot providednot providednot providednot provided0.000139not providednot provided

From GeneDx, SCV000329870.7

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

Description

Cryptic splice site that introduces a premature stop codon in gene for which loss-of-function is a known mechanism of disease (Oliveira et al., 2016); Not observed at significant frequency in large population cohorts (Lek et al., 2016); This variant is associated with the following publications: (PMID: 9536098, 17576681, 32721234, 32222963, 26841830, 26403434, 25205138)

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

From EGL Genetic Diagnostics, Eurofins Clinical Diagnostics, SCV000705513.2

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not provided1not providednot providedclinical testingnot provided
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot provided1not providednot providednot provided

Last Updated: Nov 27, 2021

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