NM_001127222.2(CACNA1A):c.3057G>A (p.Arg1019=) AND not specified

Clinical significance:Benign (Last evaluated: May 3, 2021)

Review status:2 stars out of maximum of 4 stars

criteria provided, multiple submitters, no conflicts

Based on:
6 submissions [Details]
Record status:
current
Accession:
RCV000116523.13

Allele description [Variation Report for NM_001127222.2(CACNA1A):c.3057G>A (p.Arg1019=)]

NM_001127222.2(CACNA1A):c.3057G>A (p.Arg1019=)

Gene:
CACNA1A:calcium voltage-gated channel subunit alpha1 A [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
19p13.13
Genomic location:
Preferred name:
NM_001127222.2(CACNA1A):c.3057G>A (p.Arg1019=)
HGVS:
  • NC_000019.10:g.13298576C>T
  • NG_011569.1:g.212885G>A
  • NM_000068.4:c.3069G>A
  • NM_001127221.1:c.3060G>A
  • NM_001127222.2:c.3057G>AMANE SELECT
  • NM_001174080.2:c.3060G>A
  • NM_023035.3:c.3069G>A
  • NP_000059.3:p.Arg1023=
  • NP_001120693.1:p.Arg1020=
  • NP_001120694.1:p.Arg1019=
  • NP_001167551.1:p.Arg1020=
  • NP_075461.2:p.Arg1023=
  • LRG_7t1:c.3060G>A
  • LRG_7:g.212885G>A
  • LRG_7p1:p.Arg1020=
  • NC_000019.9:g.13409390C>T
  • NM_000068.2:c.3060G>A
  • NM_001127222.1:c.3057G>A
  • NP_001120693.1:p.(=)
  • p.Arg1020Arg
Links:
dbSNP: rs16025
NCBI 1000 Genomes Browser:
rs16025
Molecular consequence:
  • NM_000068.4:c.3069G>A - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001127221.1:c.3060G>A - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001127222.2:c.3057G>A - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001174080.2:c.3060G>A - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_023035.3:c.3069G>A - synonymous variant - [Sequence Ontology: SO:0001819]
Observations:
6

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
SCV000150472Genetic Services Laboratory, University of Chicagono assertion criteria providedLikely benigngermlineclinical testing

SCV000202321EGL Genetic Diagnostics, Eurofins Clinical Diagnosticscriteria provided, single submitter
Benign
(Mar 18, 2014)
germlineclinical testing

Citation Link,

SCV000306695PreventionGenetics,PreventionGeneticscriteria provided, single submitter
Benigngermlineclinical testing

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

SCV000518852GeneDxcriteria provided, single submitter
Benign
(Jan 8, 2016)
germlineclinical testing

Citation Link,

SCV000841259Athena Diagnostics Inccriteria provided, single submitter
Benign
(May 3, 2021)
unknownclinical testing

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

SCV001744040Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen - VKGL Data-share Consensusno assertion criteria providedBenigngermlineclinical testing

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineyesnot providednot providednot providednot providednot providedclinical testing
not providedgermlineunknown6not providednot providednot providednot providedclinical testing
not providedunknownunknownnot 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, SCV000150472.2

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

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.

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

From EGL Genetic Diagnostics, Eurofins Clinical Diagnostics, SCV000202321.7

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not provided6not providednot providedclinical testingnot provided
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot provided6not providednot providednot provided

From PreventionGenetics,PreventionGenetics, SCV000306695.1

#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, SCV000518852.4

#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, SCV000841259.3

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

From Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen - VKGL Data-share Consensus, SCV001744040.3

#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: Sep 18, 2021

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