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dbSNP Short Genetic Variations

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.


Current Build 151

Released July 17, 2018

Homo sapiens
chr16:57459583 (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.

Variation Type
SNV Single Nucleotide Variation
T=0.00001 (3/246254, GnomAD)
T=0.00001 (1/125568, TOPMED)
Clinical Significance
Reported in ClinVar
Gene : Consequence
COQ9 : Stop Gained
2 citations
Genomic View
See rs on genome

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 16 NC_000016.10:g.57459583C>T
GRCh37.p13 chr 16 NC_000016.9:g.57493495C>T
COQ9 RefSeqGene NG_027696.1:g.17159C>T
Gene: COQ9, coenzyme Q9 (plus strand)
Molecule type Change Amino acid[Codon] SO Term
COQ9 transcript NM_020312.3:c.730C>T R [CGA] > * [TGA] Coding Sequence Variant
ubiquinone biosynthesis protein COQ9, mitochondrial precursor NP_064708.1:p.Arg...


R (Arg) > * (Ter) Stop Gained

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: 15470 )
ClinVar Accession Disease Names Clinical Significance
RCV000000459.4 Coenzyme Q10 deficiency, primary, 5 Pathogenic

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").

Study Population Group Sample Size Ref Allele Alt Allele
The Genome Aggregation Database Global Study-wide 246254 C=0.99999 T=0.00001
The Genome Aggregation Database European Sub 134002 C=0.99999 T=0.00001
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 15304 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

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 16 NC_000016.10:g.57459583C= NC_000016.10:g.57459583C>T
GRCh37.p13 chr 16 NC_000016.9:g.57493495C= NC_000016.9:g.57493495C>T
COQ9 RefSeqGene NG_027696.1:g.17159C= NG_027696.1:g.17159C>T
COQ9 transcript NM_020312.3:c.730C= NM_020312.3:c.730C>T
ubiquinone biosynthesis protein COQ9, mitochondrial precursor NP_064708.1:p.Arg244= NP_064708.1:p.Arg244Ter

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#.

2 Frequency, 6 SubSNP, 1 ClinVar submissions
No Submitter Submission ID Date (Build)
1 NCBI-CURATED-RECORDS ss537713080 Jan 04, 2013 (137)
2 ILLUMINA ss1959682443 Feb 12, 2016 (147)
3 HUMAN_LONGEVITY ss2212476277 Dec 20, 2016 (150)
4 GNOMAD ss2742010870 Nov 08, 2017 (151)
5 ILLUMINA ss3021710353 Nov 08, 2017 (151)
6 TOPMED ss3247541496 Nov 08, 2017 (151)
7 The Genome Aggregation Database NC_000016.9 - 57493495 Jul 20, 2018 (151)
8 Trans-Omics for Precision Medicine NC_000016.10 - 57459583 Jul 20, 2018 (151)
9 ClinVar RCV000000459.4 Jul 20, 2018 (151)

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
11025605, ss1959682443, ss2742010870, ss3021710353 NC_000016.9:57493494:C= NC_000016.10:57459582:C= (self)
145036104, ss537713080, ss2212476277, ss3247541496 NC_000016.10:57459582:C= NC_000016.10:57459582:C= (self)
11025605, ss1959682443, ss2742010870, ss3021710353 NC_000016.9:57493494:C>T NC_000016.10:57459582:C>T (self)
RCV000000459.4, 145036104, ss537713080, ss2212476277, ss3247541496 NC_000016.10:57459582:C>T NC_000016.10:57459582:C>T (self)

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

2 citations for rs267606751
PMID Title Author Year Journal
19375058 A nonsense mutation in COQ9 causes autosomal-recessive neonatal-onset primary coenzyme Q10 deficiency: a potentially treatable form of mitochondrial disease. Duncan AJ et al. 2009 American journal of human genetics
20495179 Reactive oxygen species, oxidative stress, and cell death correlate with level of CoQ10 deficiency. Quinzii CM et al. 2010 FASEB journal

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