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NM_001281463.1(SMC1A):c.1188+4G>A

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Interpretation:
Uncertain significance​

Review status:
criteria provided, multiple submitters, no conflicts
Submissions:
3 (Most recent: Mar 5, 2021)
Last evaluated:
Sep 8, 2020
Accession:
VCV000588589.5
Variation ID:
588589
Description:
single nucleotide variant
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NM_001281463.1(SMC1A):c.1188+4G>A

Allele ID
580952
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
Xp11.22
Genomic location
X: 53411757 (GRCh38) GRCh38 UCSC
X: 53438707 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
LRG_773t2:c.1254+4G>A
NC_000023.10:g.53438707C>T
NC_000023.11:g.53411757C>T
... more HGVS
Protein change
-
Other names
-
Canonical SPDI
NC_000023.11:53411756:C:T
Functional consequence
-
Global minor allele frequency (GMAF)
0.00026 (T)

Allele frequency
Exome Aggregation Consortium (ExAC) 0.00001
Trans-Omics for Precision Medicine (TOPMed) 0.00002
The Genome Aggregation Database (gnomAD), exomes 0.00001
1000 Genomes Project 0.00026
Links
dbSNP: rs781824288
Varsome
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Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Uncertain significance 2 criteria provided, multiple submitters, no conflicts Sep 8, 2020 RCV001301464.2
Uncertain significance 1 criteria provided, single submitter Dec 23, 2016 RCV000717728.1
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Gene OMIM ClinGen Gene Dosage Sensitivity Curation Variation viewer Related variants
HI score Help TS score Help Within gene All
SMC1A Sufficient evidence for dosage pathogenicity No evidence available GRCh38
GRCh37
453 610

Submitted interpretations and evidence

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Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Uncertain significance
(Dec 23, 2016)
criteria provided, single submitter
Method: clinical testing
History of neurodevelopmental disorder
Allele origin: germline
Ambry Genetics
Accession: SCV000848586.3
Submitted: (Nov 30, 2020)
Evidence details
Comment:
The c.1254+4G>A intronic variant results from a G to A substitution 4 nucleotides after coding exon 7 in the SMC1A gene. This nucleotide position is … (more)
Uncertain significance
(Sep 08, 2020)
criteria provided, single submitter
Method: clinical testing
Congenital muscular hypertrophy-cerebral syndrome
Allele origin: germline
Invitae
Accession: SCV001490634.1
Submitted: (Jan 07, 2021)
Evidence details
Publications
PubMed (2)
Comment:
This sequence change falls in intron 7 of the SMC1A gene. It does not directly change the encoded amino acid sequence of the SMC1A protein, … (more)
Uncertain significance
(Aug 08, 2018)
criteria provided, single submitter
Method: clinical testing
Congenital muscular hypertrophy-cerebral syndrome
Allele origin: maternal
Baylor Genetics
Accession: SCV001527402.1
Submitted: (Mar 05, 2021)
Evidence details
Comment:
This variant was determined to be of uncertain significance according to ACMG Guidelines, 2015 [PMID:25741868].

Functional evidence

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There is no functional evidence in ClinVar for this variation. If you have generated functional data for this variation, please consider submitting that data to ClinVar.

Citations for this variant

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Title Author Journal Year Link
Aberrant 5' splice sites in human disease genes: mutation pattern, nucleotide structure and comparison of computational tools that predict their utilization. Buratti E Nucleic acids research 2007 PMID: 17576681
Statistical features of human exons and their flanking regions. Zhang MQ Human molecular genetics 1998 PMID: 9536098

Text-mined citations for rs781824288...

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These citations are identified by LitVar using the rs number, so they may include citations for more than one variant at this location. Please review the LitVar results carefully for your variant of interest.

Record last updated Oct 08, 2021