NM_001367721.1(CASK):c.2040-9A>G AND not specified

Clinical significance:Benign/Likely benign (Last evaluated: Apr 14, 2017)

Review status:2 stars out of maximum of 4 stars

criteria provided, multiple submitters, no conflicts

Based on:
3 submissions [Details]
Record status:
current
Accession:
RCV000145396.4

Allele description [Variation Report for NM_001367721.1(CASK):c.2040-9A>G]

NM_001367721.1(CASK):c.2040-9A>G

Gene:
CASK:calcium/calmodulin dependent serine protein kinase [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
Xp11.4
Genomic location:
Preferred name:
NM_001367721.1(CASK):c.2040-9A>G
HGVS:
  • NC_000023.11:g.41542815T>C
  • NG_016754.1:g.385220A>G
  • NG_016754.2:g.385220A>G
  • NM_001126054.2:c.1971-9A>G
  • NM_001126055.2:c.1953-9A>G
  • NM_001367721.1:c.2040-9A>GMANE SELECT
  • NM_003688.3:c.2040-9A>G
  • NC_000023.10:g.41402068T>C
Links:
dbSNP: rs138290714
NCBI 1000 Genomes Browser:
rs138290714
Molecular consequence:
  • NM_001126054.2:c.1971-9A>G - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001126055.2:c.1953-9A>G - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001367721.1:c.2040-9A>G - intron variant - [Sequence Ontology: SO:0001627]
  • NM_003688.3:c.2040-9A>G - intron variant - [Sequence Ontology: SO:0001627]

Condition(s)

Synonyms:
AllHighlyPenetrant
Identifiers:
MedGen: CN169374

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV000192484Genetic Services Laboratory,University of Chicagocriteria provided, single submitter
Likely benign
(Jul 21, 2014)
germlineclinical testing

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

SCV000522094GeneDxcriteria provided, single submitter
Benign
(Mar 22, 2016)
germlineclinical testing

Citation Link,

SCV000612649Athena Diagnostics Inccriteria provided, single submitter
Benign
(Apr 14, 2017)
germlineclinical testing

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

Description

Likely benign based on allele frequency in 1000 Genomes Project or ESP global frequency and its presence in a patient with a rare or unrelated disease phenotype. NOT Sanger confirmed

SCV000192484

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical testing
not providedgermlineyesnot providednot 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

A Standardized DNA Variant Scoring System for Pathogenicity Assessments in Mendelian Disorders.

Karbassi I, Maston GA, Love A, DiVincenzo C, Braastad CD, Elzinga CD, Bright AR, Previte D, Zhang K, Rowland CM, McCarthy M, Lapierre JL, Dubois F, Medeiros KA, Batish SD, Jones J, Liaquat K, Hoffman CA, Jaremko M, Wang Z, Sun W, Buller-Burckle A, et al.

Hum Mutat. 2016 Jan;37(1):127-34. doi: 10.1002/humu.22918. Epub 2015 Oct 29.

PubMed [citation]
PMID:
26467025
PMCID:
PMC4737317

Details of each submission

From Genetic Services Laboratory,University of Chicago, SCV000192484.1

#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 GeneDx, SCV000522094.4

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

Description

This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease.

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

From Athena Diagnostics Inc, SCV000612649.1

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

Last Updated: Nov 27, 2021

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