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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 Aliases 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.

rs200915680

Current Build 153

Released July 9, 2019

Organism
Homo sapiens
Position
chr11:75399523 (GRCh38.p12) 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>G / C>T
Variation Type
SNV Single Nucleotide Variation
Frequency
T=0.00007 (9/125568, TOPMED)
T=0.0000 (1/31398, GnomAD)
T=0.0001 (1/12986, GO-ESP) (+ 1 more)
T=0.000 (1/5008, 1000G)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
RPS3 : 5 Prime UTR Variant
SNORD15A : 2KB Upstream Variant
Publications
0 citations
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.p12 chr 11 NC_000011.10:g.75399523C>G
GRCh38.p12 chr 11 NC_000011.10:g.75399523C>T
GRCh37.p13 chr 11 NC_000011.9:g.75110567C>G
GRCh37.p13 chr 11 NC_000011.9:g.75110567C>T
Gene: RPS3, ribosomal protein S3 (plus strand)
Molecule type Change Amino acid[Codon] SO Term
RPS3 transcript variant 4 NM_001260507.1:c.-272= N/A 5 Prime UTR Variant
RPS3 transcript variant 1 NM_001005.5:c.-25= N/A 5 Prime UTR Variant
RPS3 transcript variant 3 NM_001260506.2:c.-25= N/A 5 Prime UTR Variant
RPS3 transcript variant 2 NM_001256802.2:c.-25= N/A 5 Prime UTR Variant
Gene: SNORD15A, small nucleolar RNA, C/D box 15A (plus strand) : 2KB Upstream Variant
Molecule type Change Amino acid[Codon] SO Term
SNORD15A transcript NR_000005.1:n. N/A Upstream 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.

Not Reported in ClinVar
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
TopMed Global Study-wide 125568 C=0.99992 G=0.00001, T=0.00007
gnomAD - Genomes Global Study-wide 31398 C=1.0000 T=0.0000
gnomAD - Genomes European Sub 18902 C=1.0000 T=0.0000
gnomAD - Genomes African Sub 8710 C=1.000 T=0.000
gnomAD - Genomes East Asian Sub 1560 C=0.999 T=0.001
gnomAD - Genomes Other Sub 1088 C=1.000 T=0.000
gnomAD - Genomes American Sub 848 C=1.00 T=0.00
gnomAD - Genomes Ashkenazi Jewish Sub 290 C=1.00 T=0.00
GO Exome Sequencing Project Global Study-wide 12986 C=0.9999 T=0.0001
GO Exome Sequencing Project European American Sub 8586 C=1.000 T=0.000
GO Exome Sequencing Project African American Sub 4400 C=1.000 T=0.000
1000Genomes Global Study-wide 5008 C=1.000 T=0.000
1000Genomes African Sub 1322 C=1.000 T=0.000
1000Genomes East Asian Sub 1008 C=0.999 T=0.001
1000Genomes Europe Sub 1006 C=1.000 T=0.000
1000Genomes South Asian Sub 978 C=1.00 T=0.00
1000Genomes American Sub 694 C=1.00 T=0.00
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= G T Note
GRCh38.p12 chr 11 NC_000011.10:g.75...

NC_000011.10:g.75399523=

NC_000011.10:g.75...

NC_000011.10:g.75399523C>G

NC_000011.10:g.75...

NC_000011.10:g.75399523C>T

GRCh37.p13 chr 11 NC_000011.9:g.751...

NC_000011.9:g.75110567=

NC_000011.9:g.751...

NC_000011.9:g.75110567C>G

NC_000011.9:g.751...

NC_000011.9:g.75110567C>T

RPS3 transcript variant 1 NM_001005.5:c.-25= NM_001005.5:c.-25C>G NM_001005.5:c.-25C>T
RPS3 transcript variant 1 NM_001005.4:c.-25= NM_001005.4:c.-25C>G NM_001005.4:c.-25C>T
RPS3 transcript variant 3 NM_001260506.1:c....

NM_001260506.1:c.-25=

NM_001260506.1:c....

NM_001260506.1:c.-25C>G

NM_001260506.1:c....

NM_001260506.1:c.-25C>T

RPS3 transcript variant 3 NM_001260506.2:c....

NM_001260506.2:c.-25=

NM_001260506.2:c....

NM_001260506.2:c.-25C>G

NM_001260506.2:c....

NM_001260506.2:c.-25C>T

RPS3 transcript variant 4 NM_001260507.1:c....

NM_001260507.1:c.-272=

NM_001260507.1:c....

NM_001260507.1:c.-272C>G

NM_001260507.1:c....

NM_001260507.1:c.-272C>T

RPS3 transcript variant 2 NM_001256802.1:c....

NM_001256802.1:c.-25=

NM_001256802.1:c....

NM_001256802.1:c.-25C>G

NM_001256802.1:c....

NM_001256802.1:c.-25C>T

RPS3 transcript variant 2 NM_001256802.2:c....

NM_001256802.2:c.-25=

NM_001256802.2:c....

NM_001256802.2:c.-25C>G

NM_001256802.2:c....

NM_001256802.2:c.-25C>T

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#.

12 SubSNP, 8 Frequency submissions
No Submitter Submission ID Date (Build)
1 1000GENOMES ss488971828 May 04, 2012 (137)
2 NHLBI-ESP ss713037279 Apr 25, 2013 (138)
3 1000GENOMES ss1341918372 Aug 21, 2014 (142)
4 EVA_EXAC ss1690550358 Apr 01, 2015 (144)
5 EVA_EXAC ss1690550359 Apr 01, 2015 (144)
6 HUMAN_LONGEVITY ss2183609406 Dec 20, 2016 (150)
7 GNOMAD ss2739255254 Nov 08, 2017 (151)
8 GNOMAD ss2748699124 Nov 08, 2017 (151)
9 GNOMAD ss2901506170 Nov 08, 2017 (151)
10 TOPMED ss3149605583 Nov 08, 2017 (151)
11 TOPMED ss3149605584 Nov 08, 2017 (151)
12 EVA ss3749491716 Jul 13, 2019 (153)
13 1000Genomes NC_000011.9 - 75110567 Oct 12, 2018 (152)
14 ExAC

Submission ignored due to conflicting rows:
Row 819328 (NC_000011.9:75110566:C:C 119595/119596, NC_000011.9:75110566:C:G 1/119596)
Row 819329 (NC_000011.9:75110566:C:C 119592/119596, NC_000011.9:75110566:C:T 4/119596)

- Oct 12, 2018 (152)
15 ExAC

Submission ignored due to conflicting rows:
Row 819328 (NC_000011.9:75110566:C:C 119595/119596, NC_000011.9:75110566:C:G 1/119596)
Row 819329 (NC_000011.9:75110566:C:C 119592/119596, NC_000011.9:75110566:C:T 4/119596)

- Oct 12, 2018 (152)
16 gnomAD - Genomes NC_000011.9 - 75110567 Jul 13, 2019 (153)
17 gnomAD - Exomes

Submission ignored due to conflicting rows:
Row 8471761 (NC_000011.9:75110566:C:C 250555/250556, NC_000011.9:75110566:C:G 1/250556)
Row 8471762 (NC_000011.9:75110566:C:C 250546/250556, NC_000011.9:75110566:C:T 10/250556)

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

Submission ignored due to conflicting rows:
Row 8471761 (NC_000011.9:75110566:C:C 250555/250556, NC_000011.9:75110566:C:G 1/250556)
Row 8471762 (NC_000011.9:75110566:C:C 250546/250556, NC_000011.9:75110566:C:T 10/250556)

- Jul 13, 2019 (153)
19 GO Exome Sequencing Project NC_000011.9 - 75110567 Oct 12, 2018 (152)
20 TopMed NC_000011.10 - 75399523 Oct 12, 2018 (152)
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
ss1690550359, ss2739255254 NC_000011.9:75110566:C:G NC_000011.10:75399522:C:G (self)
66757462, ss3149605583 NC_000011.10:75399522:C:G NC_000011.10:75399522:C:G (self)
54462582, 148742188, 1112280, ss488971828, ss713037279, ss1341918372, ss1690550358, ss2739255254, ss2748699124, ss2901506170, ss3749491716 NC_000011.9:75110566:C:T NC_000011.10:75399522:C:T (self)
66757462, ss2183609406, ss3149605584 NC_000011.10:75399522:C:T NC_000011.10:75399522: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.

No publications for rs200915680

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.post308+0fe9b3b