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NM_001127222.2(CACNA1A):c.540-20T>C AND not specified

Germline classification:
Likely benign (1 submission)
Last evaluated:
Oct 16, 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:
RCV003403716.1

Allele description [Variation Report for NM_001127222.2(CACNA1A):c.540-20T>C]

NM_001127222.2(CACNA1A):c.540-20T>C

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.540-20T>C
HGVS:
  • NC_000019.10:g.13371799A>G
  • NG_011569.1:g.139662T>C
  • NM_000068.4:c.540-20T>C
  • NM_001127221.2:c.540-20T>C
  • NM_001127222.2:c.540-20T>CMANE SELECT
  • NM_001174080.2:c.540-20T>C
  • NM_023035.3:c.540-20T>C
  • LRG_7:g.139662T>C
  • NC_000019.9:g.13482613A>G
Links:
dbSNP: rs756413933
NCBI 1000 Genomes Browser:
rs756413933
Molecular consequence:
  • NM_000068.4:c.540-20T>C - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001127221.2:c.540-20T>C - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001127222.2:c.540-20T>C - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001174080.2:c.540-20T>C - intron variant - [Sequence Ontology: SO:0001627]
  • NM_023035.3:c.540-20T>C - intron variant - [Sequence Ontology: SO:0001627]

Condition(s)

Synonyms:
AllHighlyPenetrant
Identifiers:
MedGen: CN169374

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Assertion and evidence details

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Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV004122930Women's Health and Genetics/Laboratory Corporation of America, LabCorp
criteria provided, single submitter

(LabCorp Variant Classification Summary - May 2015)		Likely benign
(Oct 16, 2023) 		germlineclinical testing

Citation Link

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Summary from all submissions

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

Details of each submission

From Women's Health and Genetics/Laboratory Corporation of America, LabCorp, SCV004122930.1

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

Description

Variant summary: CACNA1A c.540-20T>C alters a non-conserved nucleotide located at a position not widely known to affect splicing. Consensus agreement among computation tools predict no significant impact on normal splicing. However, these predictions have yet to be confirmed by functional studies. The variant allele was found at a frequency of 5.5e-05 in 164796 control chromosomes (gnomAD). The available data on variant occurrences in the general population are insufficient to allow any conclusion about variant significance. To our knowledge, no occurrence of c.540-20T>C in individuals affected with Epileptic Encephalopathy, Early Infantile, 42 and no experimental evidence demonstrating its impact on protein function have been reported. One submitter has cited clinical-significance assessments for this variant to ClinVar after 2014 and has classified the variant as likely benign. Based on the evidence outlined above, the variant was classified as likely benign.

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

Last Updated: Mar 5, 2024