NM_001165963.4(SCN1A):c.4548G>A (p.Ser1516=) AND not specified

Clinical significance:Benign (Last evaluated: Jan 7, 2016)

Review status:2 stars out of maximum of 4 stars

criteria provided, multiple submitters, no conflicts

Based on:
2 submissions [Details]
Record status:

Allele description [Variation Report for NM_001165963.4(SCN1A):c.4548G>A (p.Ser1516=)]

NM_001165963.4(SCN1A):c.4548G>A (p.Ser1516=)

SCN1A:sodium voltage-gated channel alpha subunit 1 [Gene - OMIM - HGNC]
LOC102724058:uncharacterized LOC102724058 [Gene]
Variant type:
single nucleotide variant
Cytogenetic location:
Genomic location:
Preferred name:
NM_001165963.4(SCN1A):c.4548G>A (p.Ser1516=)
Other names:
  • NC_000002.12:g.165996046C>T
  • NG_011906.1:g.82594G>A
  • NM_001165963.4:c.4548G>AMANE SELECT
  • NM_001165963.4:c.4548G>A
  • NM_001165964.3:c.4464G>A
  • NM_001202435.3:c.4548G>A
  • NM_001353948.2:c.4548G>A
  • NM_001353949.2:c.4515G>A
  • NM_001353950.2:c.4515G>A
  • NM_001353951.2:c.4515G>A
  • NM_001353952.2:c.4515G>A
  • NM_001353954.2:c.4512G>A
  • NM_001353955.2:c.4512G>A
  • NM_001353957.2:c.4464G>A
  • NM_001353958.2:c.4464G>A
  • NM_001353960.2:c.4461G>A
  • NM_001353961.2:c.2106G>A
  • NM_006920.6:c.4515G>A
  • NP_001159435.1:p.Ser1516=
  • NP_001159436.1:p.Ser1488=
  • NP_001189364.1:p.Ser1516=
  • NP_001340877.1:p.Ser1516=
  • NP_001340878.1:p.Ser1505=
  • NP_001340879.1:p.Ser1505=
  • NP_001340880.1:p.Ser1505=
  • NP_001340881.1:p.Ser1505=
  • NP_001340883.1:p.Ser1504=
  • NP_001340884.1:p.Ser1504=
  • NP_001340886.1:p.Ser1488=
  • NP_001340887.1:p.Ser1488=
  • NP_001340889.1:p.Ser1487=
  • NP_001340890.1:p.Ser702=
  • NP_008851.3:p.Ser1505=
  • LRG_8t1:c.4515G>A
  • LRG_8:g.82594G>A
  • NC_000002.11:g.166852556C>T
  • NM_001165963.1:c.4548G>A
  • NM_006920.4:c.4515G>A
  • NR_148667.2:n.4965G>A
dbSNP: rs78041051
NCBI 1000 Genomes Browser:
Molecular consequence:
  • NR_148667.2:n.4965G>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NM_001165963.4:c.4548G>A - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001165964.3:c.4464G>A - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001202435.3:c.4548G>A - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001353948.2:c.4548G>A - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001353949.2:c.4515G>A - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001353950.2:c.4515G>A - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001353951.2:c.4515G>A - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001353952.2:c.4515G>A - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001353954.2:c.4512G>A - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001353955.2:c.4512G>A - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001353957.2:c.4464G>A - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001353958.2:c.4464G>A - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001353960.2:c.4461G>A - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001353961.2:c.2106G>A - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_006920.6:c.4515G>A - synonymous variant - [Sequence Ontology: SO:0001819]


MedGen: CN169374

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
SCV000171474GeneDxcriteria provided, single submitter
(Jul 25, 2013)
germlineclinical testing

Citation Link,

SCV000228128EGL Genetic Diagnostics, Eurofins Clinical Diagnosticscriteria provided, single submitter
(Jan 7, 2016)
germlineclinical testing

Citation Link

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknown1not providednot providednot providednot providedclinical testing
not providedgermlineyesnot providednot providednot providednot providednot providedclinical testing

Details of each submission

From GeneDx, SCV000171474.12

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


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.

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

From EGL Genetic Diagnostics, Eurofins Clinical Diagnostics, SCV000228128.5

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not provided1not providednot providedclinical testingnot provided
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot provided1not providednot providednot provided

Last Updated: Jun 14, 2021

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