NM_001281463.1(SMC1A):c.549+5G>A AND not provided

Clinical significance:Likely pathogenic (Last evaluated: May 23, 2016)

Review status:1 star out of maximum of 4 stars

criteria provided, single submitter

Based on:
1 submission [Details]
Record status:

Allele description [Variation Report for NM_001281463.1(SMC1A):c.549+5G>A]


SMC1A:structural maintenance of chromosomes 1A [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
Genomic location:
Preferred name:
  • NC_000023.11:g.53413227C>T
  • NG_006988.2:g.14444G>A
  • NM_001281463.1:c.549+5G>A
  • NM_006306.3:c.615+5G>A
  • LRG_773t1:c.549+5G>A
  • LRG_773t2:c.615+5G>A
  • LRG_773:g.14444G>A
  • NC_000023.10:g.53440177C>T
  • NM_006306.2:c.615+5G>A
dbSNP: rs1064795049
NCBI 1000 Genomes Browser:
Molecular consequence:
  • NM_001281463.1:c.549+5G>A - intron variant - [Sequence Ontology: SO:0001627]
  • NM_006306.3:c.615+5G>A - intron variant - [Sequence Ontology: SO:0001627]


MedGen: CN517202

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
SCV000570468GeneDxcriteria provided, single submitter
Likely pathogenic
(May 23, 2016)
germlineclinical testing

Citation Link

Summary from all submissions

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

Details of each submission

From GeneDx, SCV000570468.4

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


The c.615+5G>A variant in the SMC1A gene has not been reported previously as a pathogenic variant nor as a benign variant, to our knowledge. This variant is predicted to damage the natural splice acceptor site of intron 4, which may cause abnormal gene splicing. However, in the absence of RNA/functional studies, the actual effect of this sequence change in this individual is unknown. The c.615+5G>A variant was not observed in approximately 6500 individuals of European and African American ancestry in the NHLBI Exome Sequencing Project, indicating it is not a common benign variant in these populations. The c.615+5G>A variant is a strong candidate for a pathogenic variant, however the possibility it may be a rare benign variant cannot be excluded.

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

Last Updated: Feb 27, 2021

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