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dbSNP Short Genetic Variations

Welcome to the Reference SNP (rs) Report

All alleles are reported in the Forward orientation. Click on the Variant Details tab for details on Genomic Placement, Gene, and Amino Acid changes. HGVS names are in the HGVS tab.

Reference SNP (rs) Report

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.

rs148370803

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr17:4901620 (GRCh38.p14) 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
T>A / T>C
Variation Type
SNV Single Nucleotide Variation
Frequency
A=0.00016 (7/44294, ALFA)
A=0.00015 (2/13006, GO-ESP)
Clinical Significance
Reported in ClinVar
Gene : Consequence
CHRNE : Missense Variant
C17orf107 : Non Coding Transcript Variant
Publications
0 citations
Genomic View
See rs on genome

ALFA Allele Frequency
The ALFA project provide aggregate allele frequency from dbGaP. More information is available on the project page including descriptions, data access, and terms of use.

Release Version: 20230706150541
Population Group Sample Size Ref Allele Alt Allele
Total Global 44294 T=0.99984 A=0.00016, C=0.00000
European Sub 32564 T=0.99979 A=0.00021, C=0.00000
African Sub 3512 T=1.0000 A=0.0000, C=0.0000
African Others Sub 122 T=1.000 A=0.000, C=0.000
African American Sub 3390 T=1.0000 A=0.0000, C=0.0000
Asian Sub 168 T=1.000 A=0.000, C=0.000
East Asian Sub 112 T=1.000 A=0.000, C=0.000
Other Asian Sub 56 T=1.00 A=0.00, C=0.00
Latin American 1 Sub 486 T=1.000 A=0.000, C=0.000
Latin American 2 Sub 626 T=1.000 A=0.000, C=0.000
South Asian Sub 98 T=1.00 A=0.00, C=0.00
Other Sub 6840 T=1.0000 A=0.0000, C=0.0000


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").

Download
Study Population Group Sample Size Ref Allele Alt Allele
Allele Frequency Aggregator Total Global 44294 T=0.99984 A=0.00016, C=0.00000
Allele Frequency Aggregator European Sub 32564 T=0.99979 A=0.00021, C=0.00000
Allele Frequency Aggregator Other Sub 6840 T=1.0000 A=0.0000, C=0.0000
Allele Frequency Aggregator African Sub 3512 T=1.0000 A=0.0000, C=0.0000
Allele Frequency Aggregator Latin American 2 Sub 626 T=1.000 A=0.000, C=0.000
Allele Frequency Aggregator Latin American 1 Sub 486 T=1.000 A=0.000, C=0.000
Allele Frequency Aggregator Asian Sub 168 T=1.000 A=0.000, C=0.000
Allele Frequency Aggregator South Asian Sub 98 T=1.00 A=0.00, C=0.00
GO Exome Sequencing Project Global Study-wide 13006 T=0.99985 A=0.00015
GO Exome Sequencing Project European American Sub 8600 T=0.9998 A=0.0002
GO Exome Sequencing Project African American Sub 4406 T=1.0000 A=0.0000
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.p14 chr 17 NC_000017.11:g.4901620T>A
GRCh38.p14 chr 17 NC_000017.11:g.4901620T>C
GRCh37.p13 chr 17 NC_000017.10:g.4804915T>A
GRCh37.p13 chr 17 NC_000017.10:g.4804915T>C
CHRNE RefSeqGene (LRG_1254) NG_008029.2:g.6456A>T
CHRNE RefSeqGene (LRG_1254) NG_008029.2:g.6456A>G
Gene: C17orf107, chromosome 17 open reading frame 107 (plus strand)
Molecule type Change Amino acid[Codon] SO Term
C17orf107 transcript NM_001145536.2:c.*1087= N/A 3 Prime UTR Variant
C17orf107 transcript variant X1 XR_007065253.1:n.1887T>A N/A Non Coding Transcript Variant
C17orf107 transcript variant X1 XR_007065253.1:n.1887T>C N/A Non Coding Transcript Variant
C17orf107 transcript variant X2 XR_007065254.1:n.1887T>A N/A Non Coding Transcript Variant
C17orf107 transcript variant X2 XR_007065254.1:n.1887T>C N/A Non Coding Transcript Variant
Gene: CHRNE, cholinergic receptor nicotinic epsilon subunit (minus strand)
Molecule type Change Amino acid[Codon] SO Term
CHRNE transcript NM_000080.4:c.506A>T Q [CAG] > L [CTG] Coding Sequence Variant
acetylcholine receptor subunit epsilon precursor NP_000071.1:p.Gln169Leu Q (Gln) > L (Leu) Missense Variant
CHRNE transcript NM_000080.4:c.506A>G Q [CAG] > R [CGG] Coding Sequence Variant
acetylcholine receptor subunit epsilon precursor NP_000071.1:p.Gln169Arg Q (Gln) > R (Arg) Missense Variant
CHRNE transcript variant X1 XM_017024115.2:c.470A>T Q [CAG] > L [CTG] Coding Sequence Variant
acetylcholine receptor subunit epsilon isoform X1 XP_016879604.1:p.Gln157Leu Q (Gln) > L (Leu) Missense Variant
CHRNE transcript variant X1 XM_017024115.2:c.470A>G Q [CAG] > R [CGG] Coding Sequence Variant
acetylcholine receptor subunit epsilon isoform X1 XP_016879604.1:p.Gln157Arg Q (Gln) > R (Arg) Missense 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: A (allele ID: 346460 )
ClinVar Accession Disease Names Clinical Significance
RCV000301401.3 Congenital myasthenic syndrome Uncertain-Significance
RCV000689021.10 Congenital myasthenic syndrome 4A Conflicting-Interpretations-Of-Pathogenicity
RCV000714532.3 Congenital myasthenic syndrome 4C Uncertain-Significance
RCV000714533.3 Congenital myasthenic syndrome 4B Uncertain-Significance
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 T= A C
GRCh38.p14 chr 17 NC_000017.11:g.4901620= NC_000017.11:g.4901620T>A NC_000017.11:g.4901620T>C
GRCh37.p13 chr 17 NC_000017.10:g.4804915= NC_000017.10:g.4804915T>A NC_000017.10:g.4804915T>C
CHRNE RefSeqGene (LRG_1254) NG_008029.2:g.6456= NG_008029.2:g.6456A>T NG_008029.2:g.6456A>G
CHRNE transcript NM_000080.4:c.506= NM_000080.4:c.506A>T NM_000080.4:c.506A>G
CHRNE transcript NM_000080.3:c.506= NM_000080.3:c.506A>T NM_000080.3:c.506A>G
C17orf107 transcript NM_001145536.2:c.*1087= NM_001145536.2:c.*1087T>A NM_001145536.2:c.*1087T>C
C17orf107 transcript NM_001145536.1:c.*1087= NM_001145536.1:c.*1087T>A NM_001145536.1:c.*1087T>C
CHRNE transcript variant X1 XM_017024115.2:c.470= XM_017024115.2:c.470A>T XM_017024115.2:c.470A>G
CHRNE transcript variant X1 XM_017024115.1:c.470= XM_017024115.1:c.470A>T XM_017024115.1:c.470A>G
C17orf107 transcript variant X1 XR_007065253.1:n.1887= XR_007065253.1:n.1887T>A XR_007065253.1:n.1887T>C
C17orf107 transcript variant X2 XR_007065254.1:n.1887= XR_007065254.1:n.1887T>A XR_007065254.1:n.1887T>C
acetylcholine receptor subunit epsilon precursor NP_000071.1:p.Gln169= NP_000071.1:p.Gln169Leu NP_000071.1:p.Gln169Arg
acetylcholine receptor subunit epsilon isoform X1 XP_016879604.1:p.Gln157= XP_016879604.1:p.Gln157Leu XP_016879604.1:p.Gln157Arg
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#.

10 SubSNP, 10 Frequency, 4 ClinVar submissions
No Submitter Submission ID Date (Build)
1 NHLBI-ESP ss342441206 May 09, 2011 (134)
2 EVA_EXAC ss1692542072 Apr 01, 2015 (144)
3 EVA_EXAC ss1692542073 Apr 01, 2015 (144)
4 HUMAN_LONGEVITY ss2215150668 Dec 20, 2016 (150)
5 GNOMAD ss2749662740 Nov 08, 2017 (151)
6 GNOMAD ss2947196709 Nov 08, 2017 (151)
7 SWEGEN ss3015120589 Nov 08, 2017 (151)
8 EVA ss3825065997 Apr 27, 2020 (154)
9 TOPMED ss5027964686 Apr 26, 2021 (155)
10 TOPMED ss5027964687 Apr 26, 2021 (155)
11 ExAC

Submission ignored due to conflicting rows:
Row 2966700 (NC_000017.10:4804914:T:T 120559/120564, NC_000017.10:4804914:T:C 5/120564)
Row 2966701 (NC_000017.10:4804914:T:T 120554/120564, NC_000017.10:4804914:T:A 10/120564)

- Oct 12, 2018 (152)
12 ExAC

Submission ignored due to conflicting rows:
Row 2966700 (NC_000017.10:4804914:T:T 120559/120564, NC_000017.10:4804914:T:C 5/120564)
Row 2966701 (NC_000017.10:4804914:T:T 120554/120564, NC_000017.10:4804914:T:A 10/120564)

- Oct 12, 2018 (152)
13 gnomAD - Genomes

Submission ignored due to conflicting rows:
Row 500212872 (NC_000017.11:4901619:T:A 9/140266)
Row 500212873 (NC_000017.11:4901619:T:C 3/140266)

- Apr 26, 2021 (155)
14 gnomAD - Genomes

Submission ignored due to conflicting rows:
Row 500212872 (NC_000017.11:4901619:T:A 9/140266)
Row 500212873 (NC_000017.11:4901619:T:C 3/140266)

- Apr 26, 2021 (155)
15 gnomAD - Exomes

Submission ignored due to conflicting rows:
Row 11649477 (NC_000017.10:4804914:T:T 250054/250076, NC_000017.10:4804914:T:A 22/250076)
Row 11649478 (NC_000017.10:4804914:T:T 250061/250076, NC_000017.10:4804914:T:C 15/250076)

- Jul 13, 2019 (153)
16 gnomAD - Exomes

Submission ignored due to conflicting rows:
Row 11649477 (NC_000017.10:4804914:T:T 250054/250076, NC_000017.10:4804914:T:A 22/250076)
Row 11649478 (NC_000017.10:4804914:T:T 250061/250076, NC_000017.10:4804914:T:C 15/250076)

- Jul 13, 2019 (153)
17 GO Exome Sequencing Project NC_000017.10 - 4804915 Oct 12, 2018 (152)
18 TopMed

Submission ignored due to conflicting rows:
Row 243510348 (NC_000017.11:4901619:T:A 17/264690)
Row 243510349 (NC_000017.11:4901619:T:C 12/264690)

- Apr 26, 2021 (155)
19 TopMed

Submission ignored due to conflicting rows:
Row 243510348 (NC_000017.11:4901619:T:A 17/264690)
Row 243510349 (NC_000017.11:4901619:T:C 12/264690)

- Apr 26, 2021 (155)
20 ALFA NC_000017.11 - 4901620 Apr 26, 2021 (155)
21 ClinVar RCV000301401.3 Oct 17, 2022 (156)
22 ClinVar RCV000689021.10 Oct 17, 2022 (156)
23 ClinVar RCV000714532.3 Oct 17, 2022 (156)
24 ClinVar RCV000714533.3 Oct 17, 2022 (156)
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
1523129, ss342441206, ss1692542073, ss2749662740, ss2947196709, ss3015120589, ss3825065997 NC_000017.10:4804914:T:A NC_000017.11:4901619:T:A (self)
RCV000301401.3, RCV000689021.10, RCV000714532.3, RCV000714533.3, 2724844503, ss2215150668, ss5027964686 NC_000017.11:4901619:T:A NC_000017.11:4901619:T:A (self)
ss1692542072 NC_000017.10:4804914:T:C NC_000017.11:4901619:T:C (self)
2724844503, ss5027964687 NC_000017.11:4901619:T:C NC_000017.11:4901619:T:C (self)
Help

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

No publications for rs148370803

Help

The Flanks tab provides retrieving flanking sequences of a SNP on all molecules that have placements.

Genome context:
Select flank length:

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: 2.0.1.post761+d5e8e07