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dbSNP Short Genetic Variations

Examples: rs268, BRCA1 and more Advanced search

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.

rs187553585

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr9:5339872 (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
C>G
Variation Type
SNV Single Nucleotide Variation
Frequency
G=0.002895 (402/138876, GnomAD)
G=0.00014 (4/28258, 14KJPN)
G=0.00036 (6/16760, 8.3KJPN) (+ 4 more)
G=0.00245 (30/12232, ALFA)
G=0.0036 (23/6404, 1000G_30x)
G=0.0018 (9/5008, 1000G)
G=0.005 (1/216, Qatari)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
RLN1 : Intron Variant
RLN2 : 2KB Upstream 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 12232 C=0.99755 G=0.00245
European Sub 7752 C=0.9987 G=0.0013
African Sub 2864 C=0.9941 G=0.0059
African Others Sub 108 C=1.000 G=0.000
African American Sub 2756 C=0.9938 G=0.0062
Asian Sub 108 C=1.000 G=0.000
East Asian Sub 84 C=1.00 G=0.00
Other Asian Sub 24 C=1.00 G=0.00
Latin American 1 Sub 146 C=1.000 G=0.000
Latin American 2 Sub 610 C=0.997 G=0.003
South Asian Sub 94 C=1.00 G=0.00
Other Sub 658 C=0.998 G=0.002


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
gnomAD - Genomes Global Study-wide 138876 C=0.997105 G=0.002895
gnomAD - Genomes European Sub 75914 C=0.99942 G=0.00058
gnomAD - Genomes African Sub 40788 C=0.99242 G=0.00758
gnomAD - Genomes American Sub 13594 C=0.99831 G=0.00169
gnomAD - Genomes Ashkenazi Jewish Sub 3322 C=0.9955 G=0.0045
gnomAD - Genomes East Asian Sub 3130 C=0.9997 G=0.0003
gnomAD - Genomes Other Sub 2128 C=0.9953 G=0.0047
14KJPN JAPANESE Study-wide 28258 C=0.99986 G=0.00014
8.3KJPN JAPANESE Study-wide 16760 C=0.99964 G=0.00036
Allele Frequency Aggregator Total Global 12232 C=0.99755 G=0.00245
Allele Frequency Aggregator European Sub 7752 C=0.9987 G=0.0013
Allele Frequency Aggregator African Sub 2864 C=0.9941 G=0.0059
Allele Frequency Aggregator Other Sub 658 C=0.998 G=0.002
Allele Frequency Aggregator Latin American 2 Sub 610 C=0.997 G=0.003
Allele Frequency Aggregator Latin American 1 Sub 146 C=1.000 G=0.000
Allele Frequency Aggregator Asian Sub 108 C=1.000 G=0.000
Allele Frequency Aggregator South Asian Sub 94 C=1.00 G=0.00
1000Genomes_30x Global Study-wide 6404 C=0.9964 G=0.0036
1000Genomes_30x African Sub 1786 C=0.9888 G=0.0112
1000Genomes_30x Europe Sub 1266 C=0.9992 G=0.0008
1000Genomes_30x South Asian Sub 1202 C=1.0000 G=0.0000
1000Genomes_30x East Asian Sub 1170 C=1.0000 G=0.0000
1000Genomes_30x American Sub 980 C=0.998 G=0.002
1000Genomes Global Study-wide 5008 C=0.9982 G=0.0018
1000Genomes African Sub 1322 C=0.9962 G=0.0038
1000Genomes East Asian Sub 1008 C=1.0000 G=0.0000
1000Genomes Europe Sub 1006 C=0.9990 G=0.0010
1000Genomes South Asian Sub 978 C=1.000 G=0.000
1000Genomes American Sub 694 C=0.996 G=0.004
Qatari Global Study-wide 216 C=0.995 G=0.005
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 9 NC_000009.12:g.5339872C>G
GRCh37.p13 chr 9 NC_000009.11:g.5339872C>G
Gene: RLN1, relaxin 1 (minus strand)
Molecule type Change Amino acid[Codon] SO Term
RLN1 transcript NM_006911.4:c.-126= N/A 5 Prime UTR Variant
RLN1 transcript variant X4 XM_047423706.1:c.-48+949G…

XM_047423706.1:c.-48+949G>C

 		N/A Intron Variant
RLN1 transcript variant X1 XM_047423703.1:c.-126= N/A 5 Prime UTR Variant
RLN1 transcript variant X2 XM_047423704.1:c. N/A Genic Upstream Transcript Variant
RLN1 transcript variant X3 XM_047423705.1:c. N/A Genic Upstream Transcript Variant
Gene: RLN2, relaxin 2 (minus strand) : 2KB Upstream Variant
Molecule type Change Amino acid[Codon] SO Term
RLN2 transcript variant 3 NM_001329191.2:c. N/A N/A
RLN2 transcript variant 2 NM_005059.4:c. N/A N/A
RLN2 transcript variant 1 NM_134441.3:c. N/A N/A
RLN2 transcript variant X1 XM_047423707.1:c. N/A Upstream Transcript Variant
RLN2 transcript variant X3 XM_047423709.1:c. N/A Upstream Transcript Variant
RLN2 transcript variant X2 XM_047423708.1:c. N/A N/A
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

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
GRCh38.p14 chr 9 NC_000009.12:g.5339872= NC_000009.12:g.5339872C>G
GRCh37.p13 chr 9 NC_000009.11:g.5339872= NC_000009.11:g.5339872C>G
RLN1 transcript NM_006911.4:c.-126= NM_006911.4:c.-126G>C
RLN1 transcript NM_006911.3:c.-126= NM_006911.3:c.-126G>C
RLN1 transcript variant X1 XM_047423703.1:c.-126= XM_047423703.1:c.-126G>C
RLN1 transcript variant X4 XM_047423706.1:c.-48+949= XM_047423706.1:c.-48+949G>C
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#.

14 SubSNP, 7 Frequency submissions
No Submitter Submission ID Date (Build)
1 1000GENOMES ss460895448 Sep 17, 2011 (135)
2 1000GENOMES ss1332682754 Aug 21, 2014 (142)
3 WEILL_CORNELL_DGM ss1929534496 Feb 12, 2016 (147)
4 GNOMAD ss2874819973 Nov 08, 2017 (151)
5 SWEGEN ss3004301572 Nov 08, 2017 (151)
6 TOMMO_GENOMICS ss5191844962 Apr 26, 2021 (155)
7 1000G_HIGH_COVERAGE ss5279610953 Oct 16, 2022 (156)
8 EVA ss5385698737 Oct 16, 2022 (156)
9 1000G_HIGH_COVERAGE ss5571273774 Oct 16, 2022 (156)
10 SANFORD_IMAGENETICS ss5646799045 Oct 16, 2022 (156)
11 TOMMO_GENOMICS ss5734827782 Oct 16, 2022 (156)
12 YY_MCH ss5810297756 Oct 16, 2022 (156)
13 EVA ss5828778552 Oct 16, 2022 (156)
14 EVA ss5976065146 Oct 16, 2022 (156)
15 1000Genomes NC_000009.11 - 5339872 Oct 12, 2018 (152)
16 1000Genomes_30x NC_000009.12 - 5339872 Oct 16, 2022 (156)
17 gnomAD - Genomes NC_000009.12 - 5339872 Apr 26, 2021 (155)
18 Qatari NC_000009.11 - 5339872 Apr 26, 2020 (154)
19 8.3KJPN NC_000009.11 - 5339872 Apr 26, 2021 (155)
20 14KJPN NC_000009.12 - 5339872 Oct 16, 2022 (156)
21 ALFA NC_000009.12 - 5339872 Apr 26, 2021 (155)
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
44904913, 11576426, 49814269, ss460895448, ss1332682754, ss1929534496, ss2874819973, ss3004301572, ss5191844962, ss5385698737, ss5646799045, ss5828778552, ss5976065146 NC_000009.11:5339871:C:G NC_000009.12:5339871:C:G (self)
58799709, 316541115, 68664886, 4452417583, ss5279610953, ss5571273774, ss5734827782, ss5810297756 NC_000009.12:5339871:C:G NC_000009.12:5339871:C:G (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 rs187553585

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