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dbSNP Short Genetic Variations

Reference SNP (rs) Report

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This page reports data for a single dbSNP Reference SNP variation (RefSNP or rs) from the new redesigned dbSNP build.
Top of the page reports a concise summary for the rs, with more specific details included in the corresponding tabs below.
All alleles are reported in the Forward orientation. Use the Genomic View to inspect the nucleotides flanking the variant, and its neighbors.
For more information see Help documentation.

rs372635387

Current Build 151

Released July 17, 2018

Organism
Homo sapiens
Position
chr17:4903027 (GRCh38.p7) Help

The anchor position for this RefSNP. Includes all nucleotides potentially affected by this change, thus it can differ from HGVS, which is right-shifted. See here for details.

Alleles
C>T
Variation Type
SNV Single Nucleotide Variation
Frequency
T=0.00003 (7/246218, GnomAD)
T=0.00001 (1/125568, TOPMED)
T=0.00003 (4/121150, ExAC) (+ 1 more)
T=0.0001 (1/13006, GO-ESP)
Clinical Significance
Reported in ClinVar
Gene : Consequence
CHRNE : Missense Variant
C17orf107 : 500B Downstream Variant
Publications
1 citation
Genomic View
See rs on genome
Help

Variant Details tab shows known variant placements on genomic sequences: chromosomes (NC_), RefSeqGene, pseudogenes or genomic regions (NG_), and in a separate table: on transcripts (NM_) and protein sequences (NP_). The corresponding transcript and protein locations are listed in adjacent lines, along with molecular consequences from Sequence Ontology. When no protein placement is available, only the transcript is listed. Column "Codon[Amino acid]" shows the actual base change in the format of "Reference > Alternate" allele, including the nucleotide codon change in transcripts, and the amino acid change in proteins, respectively, allowing for known ribosomal slippage sites. To view nucleotides adjacent to the variant use the Genomic View at the bottom of the page - zoom into the sequence until the nucleotides around the variant become visible.

Genomic Placements
Sequence name Change
GRCh38.p7 chr 17 NC_000017.11:g.4903027C>T
GRCh37.p13 chr 17 NC_000017.10:g.4806322C>T
CHRNE RefSeqGene (LRG_1254) NG_008029.2:g.5049G>A
Gene: C17orf107, chromosome 17 open reading frame 107 (plus strand) : 500B Downstream Variant
Molecule type Change Amino acid[Codon] SO Term
C17orf107 transcript NM_001145536.1:c. N/A Downstream Transcript Variant
Gene: CHRNE, cholinergic receptor nicotinic epsilon subunit (minus strand)
Molecule type Change Amino acid[Codon] SO Term
CHRNE transcript NM_000080.3:c.37G>A G [GGG] > R [AGG] Coding Sequence Variant
acetylcholine receptor subunit epsilon precursor NP_000071.1:p.Gly...

NP_000071.1:p.Gly13Arg

G (Gly) > R (Arg) Missense Variant
CHRNE transcript variant X1 XM_017024115.1:c. N/A Intron Variant
CHRNE transcript variant X2 XR_001752421.1:n....

XR_001752421.1:n.882G>A

N/A Non Coding Transcript Variant
Help

Clinical Significance tab shows a list of clinical significance entries from ClinVar associated with the variation, per allele. Click on the RCV accession (i.e. RCV000001615.2) or Allele ID (i.e. 12274) to access full ClinVar report.

Allele: T (allele ID: 33398 )
ClinVar Accession Disease Names Clinical Significance
RCV000020027.28 Myasthenic syndrome, congenital, 4b, fast-channel Pathogenic
RCV000559012.1 Myasthenic syndrome, congenital, 4a, slow-channel Uncertain-Significance
Help

Frequency tab displays a table of the reference and alternate allele frequencies reported by various studies and populations. Table lines, where Population="Global" refer to the entire study population, whereas lines, where Group="Sub", refer to a study-specific population subgroupings (i.e. AFR, CAU, etc.), if available. Frequency for the alternate allele (Alt Allele) is a ratio of samples observed-to-total, where the numerator (observed samples) is the number of chromosomes in the study with the minor allele present (found in "Sample size", where Group="Sub"), and the denominator (total samples) is the total number of all chromosomes in the study for the variant (found in "Sample size", where Group="Study-wide" and Population="Global").

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Study Population Group Sample Size Ref Allele Alt Allele
The Genome Aggregation Database Global Study-wide 246218 C=0.99997 T=0.00003
The Genome Aggregation Database European Sub 133974 C=0.99997 T=0.00003
The Genome Aggregation Database Asian Sub 48030 C=1.0000 T=0.0000
The Genome Aggregation Database American Sub 33582 C=1.0000 T=0.0000
The Genome Aggregation Database African Sub 15296 C=1.0000 T=0.0000
The Genome Aggregation Database Ashkenazi Jewish Sub 9850 C=1.000 T=0.000
The Genome Aggregation Database Other Sub 5486 C=1.000 T=0.000
Trans-Omics for Precision Medicine Global Study-wide 125568 C=0.99999 T=0.00001
The Exome Aggregation Consortium Global Study-wide 121150 C=0.99997 T=0.00003
The Exome Aggregation Consortium Europe Sub 73178 C=1.0000 T=0.0000
The Exome Aggregation Consortium Asian Sub 25154 C=1.0000 T=0.0000
The Exome Aggregation Consortium American Sub 11540 C=1.0000 T=0.0000
The Exome Aggregation Consortium African Sub 10376 C=1.0000 T=0.0000
The Exome Aggregation Consortium Other Sub 902 C=1.00 T=0.00
GO Exome Sequencing Project Global Study-wide 13006 C=0.9999 T=0.0001
GO Exome Sequencing Project European American Sub 8600 C=1.000 T=0.000
GO Exome Sequencing Project African American Sub 4406 C=1.000 T=0.000
Help

Aliases tab displays HGVS names representing the variant placements and allele changes on genomic, transcript and protein sequences, per allele. HGVS name is an expression for reporting sequence accession and version, sequence type, position, and allele change. The column "Note" can have two values: "diff" means that there is a difference between the reference allele (variation interval) at the placement reported in HGVS name and the reference alleles reported in other HGVS names, and "rev" means that the sequence of this variation interval at the placement reported in HGVS name is in reverse orientation to the sequence(s) of this variation in other HGVS names not labeled as "rev".

Placement C= T Note
GRCh38.p7 chr 17 NC_000017.11:g.4903027C= NC_000017.11:g.4903027C>T
GRCh37.p13 chr 17 NC_000017.10:g.4806322C= NC_000017.10:g.4806322C>T
CHRNE RefSeqGene (LRG_1254) NG_008029.2:g.5049G= NG_008029.2:g.5049G>A
CHRNE transcript NM_000080.3:c.37G= NM_000080.3:c.37G>A
CHRNE transcript variant X2 XR_001752421.1:n.882G= XR_001752421.1:n.882G>A
acetylcholine receptor subunit epsilon precursor NP_000071.1:p.Gly13= NP_000071.1:p.Gly13Arg
Help

Submissions tab displays variations originally submitted to dbSNP, now supporting this RefSNP cluster (rs). We display Submitter handle, Submission identifier, Date and Build number, when the submission appeared for the first time. Direct submissions to dbSNP have Submission ID in the form of an ss-prefixed number (ss#). Other supporting variations are listed in the table without ss#.

4 Frequency, 7 SubSNP, 2 ClinVar submissions
No Submitter Submission ID Date (Build)
1 NHLBI-ESP ss713350497 Apr 25, 2013 (138)
2 OMIM-CURATED-RECORDS ss825077124 Jun 20, 2013 (137)
3 EVA_EXAC ss1692542310 Apr 01, 2015 (144)
4 GNOMAD ss2742354113 Nov 08, 2017 (151)
5 AFFY ss2985083085 Nov 08, 2017 (151)
6 AFFY ss2985721757 Nov 08, 2017 (151)
7 TOPMED ss3256143065 Nov 08, 2017 (151)
8 The Exome Aggregation Consortium NC_000017.10 - 4806322 Jul 20, 2018 (151)
9 The Genome Aggregation Database NC_000017.10 - 4806322 Jul 20, 2018 (151)
10 GO Exome Sequencing Project NC_000017.10 - 4806322 Jul 20, 2018 (151)
11 Trans-Omics for Precision Medicine NC_000017.11 - 4903027 Jul 20, 2018 (151)
12 ClinVar RCV000020027.28 Jul 20, 2018 (151)
13 ClinVar RCV000559012.1 Jul 20, 2018 (151)
Help

History tab displays RefSNPs (Associated ID) from previous builds (Build) that now support the current RefSNP, and the dates, when the history was updated for each Associated ID (History Updated).

Added to this RefSNP Cluster:
Submission ids Observation SPDI Canonical SPDI Source RSIDs
2966972, 11368848, 1523177, ss713350497, ss1692542310, ss2742354113, ss2985083085, ss2985721757 NC_000017.10:4806321:C= NC_000017.11:4903026:C= (self)
151957581, ss825077124, ss3256143065 NC_000017.11:4903026:C= NC_000017.11:4903026:C= (self)
2966972, 11368848, 1523177, ss713350497, ss1692542310, ss2742354113, ss2985083085, ss2985721757 NC_000017.10:4806321:C>T NC_000017.11:4903026:C>T (self)
RCV000020027.28, RCV000559012.1, 151957581, ss825077124, ss3256143065 NC_000017.11:4903026:C>T NC_000017.11:4903026:C>T (self)
Help

Publications tab displays PubMed articles citing the variation as a listing of PMID, Title, Author, Year, Journal, ordered by Year, descending.

1 citation for rs372635387
PMID Title Author Year Journal
8755487 Congenital myasthenic syndrome caused by decreased agonist binding affinity due to a mutation in the acetylcholine receptor epsilon subunit. Ohno K et al. 1996 Neuron

Genomic regions, transcripts, and products
Top Help

NCBI Graphical Sequence Viewer display of the genomic region, transcripts and protein products for the reported RefSNP (rs).
Use the zoom option to view the nucleotides around the RefSNP and find other neighboring RefSNPs.
Visit Sequence Viewer for help with navigating inside the display and modifying the selection of displayed data tracks.

Software version is: 0.1.4.post833+d3ba21e