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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.

rs17325399

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr5:55111122 (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
A>G
Variation Type
SNV Single Nucleotide Variation
Frequency
G=0.041320 (10937/264690, TOPMED)
G=0.036983 (5113/138254, GnomAD)
G=0.02839 (488/17190, ALFA) (+ 7 more)
G=0.0450 (288/6404, 1000G_30x)
G=0.0387 (194/5008, 1000G)
G=0.0003 (1/3854, ALSPAC)
G=0.0000 (0/3708, TWINSUK)
G=0.005 (3/626, Chileans)
A=0.50 (8/16, SGDP_PRJ)
G=0.50 (8/16, SGDP_PRJ)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
None
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 17190 A=0.97161 G=0.02839
European Sub 11208 A=0.99973 G=0.00027
African Sub 3624 A=0.8767 G=0.1233
African Others Sub 126 A=0.857 G=0.143
African American Sub 3498 A=0.8774 G=0.1226
Asian Sub 160 A=1.000 G=0.000
East Asian Sub 102 A=1.000 G=0.000
Other Asian Sub 58 A=1.00 G=0.00
Latin American 1 Sub 212 A=0.958 G=0.042
Latin American 2 Sub 754 A=0.991 G=0.009
South Asian Sub 110 A=1.000 G=0.000
Other Sub 1122 A=0.9804 G=0.0196


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 264690 A=0.958680 G=0.041320
gnomAD - Genomes Global Study-wide 138254 A=0.963017 G=0.036983
gnomAD - Genomes European Sub 74916 A=0.99964 G=0.00036
gnomAD - Genomes African Sub 41314 A=0.88123 G=0.11877
gnomAD - Genomes American Sub 13446 A=0.99018 G=0.00982
gnomAD - Genomes Ashkenazi Jewish Sub 3322 A=0.9997 G=0.0003
gnomAD - Genomes East Asian Sub 3128 A=1.0000 G=0.0000
gnomAD - Genomes Other Sub 2128 A=0.9784 G=0.0216
Allele Frequency Aggregator Total Global 17190 A=0.97161 G=0.02839
Allele Frequency Aggregator European Sub 11208 A=0.99973 G=0.00027
Allele Frequency Aggregator African Sub 3624 A=0.8767 G=0.1233
Allele Frequency Aggregator Other Sub 1122 A=0.9804 G=0.0196
Allele Frequency Aggregator Latin American 2 Sub 754 A=0.991 G=0.009
Allele Frequency Aggregator Latin American 1 Sub 212 A=0.958 G=0.042
Allele Frequency Aggregator Asian Sub 160 A=1.000 G=0.000
Allele Frequency Aggregator South Asian Sub 110 A=1.000 G=0.000
1000Genomes_30x Global Study-wide 6404 A=0.9550 G=0.0450
1000Genomes_30x African Sub 1786 A=0.8477 G=0.1523
1000Genomes_30x Europe Sub 1266 A=0.9984 G=0.0016
1000Genomes_30x South Asian Sub 1202 A=1.0000 G=0.0000
1000Genomes_30x East Asian Sub 1170 A=1.0000 G=0.0000
1000Genomes_30x American Sub 980 A=0.986 G=0.014
1000Genomes Global Study-wide 5008 A=0.9613 G=0.0387
1000Genomes African Sub 1322 A=0.8616 G=0.1384
1000Genomes East Asian Sub 1008 A=1.0000 G=0.0000
1000Genomes Europe Sub 1006 A=0.9990 G=0.0010
1000Genomes South Asian Sub 978 A=1.000 G=0.000
1000Genomes American Sub 694 A=0.986 G=0.014
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 A=0.9997 G=0.0003
UK 10K study - Twins TWIN COHORT Study-wide 3708 A=1.0000 G=0.0000
Chileans Chilean Study-wide 626 A=0.995 G=0.005
SGDP_PRJ Global Study-wide 16 A=0.50 G=0.50
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 5 NC_000005.10:g.55111122A>G
GRCh37.p13 chr 5 NC_000005.9:g.54406950A>G
GZMA RefSeqGene NG_027996.2:g.13478A>G
GZMA RefSeqGene NG_027996.1:g.13477A>G
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 A= G
GRCh38.p14 chr 5 NC_000005.10:g.55111122= NC_000005.10:g.55111122A>G
GRCh37.p13 chr 5 NC_000005.9:g.54406950= NC_000005.9:g.54406950A>G
GZMA RefSeqGene NG_027996.2:g.13478= NG_027996.2:g.13478A>G
GZMA RefSeqGene NG_027996.1:g.13477= NG_027996.1:g.13477A>G
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#.

26 SubSNP, 9 Frequency submissions
No Submitter Submission ID Date (Build)
1 PERLEGEN ss23349458 Sep 20, 2004 (123)
2 AFFY ss66036210 Jun 24, 2010 (142)
3 AFFY ss75924946 Dec 07, 2007 (129)
4 KRIBB_YJKIM ss83236396 Dec 17, 2007 (130)
5 COMPLETE_GENOMICS ss164941108 Jul 04, 2010 (132)
6 AFFY ss169200004 Jun 24, 2010 (142)
7 1000GENOMES ss221679943 Jul 14, 2010 (132)
8 TISHKOFF ss558392275 Apr 25, 2013 (138)
9 1000GENOMES ss1315107329 Aug 21, 2014 (142)
10 EVA_UK10K_ALSPAC ss1612893178 Apr 01, 2015 (144)
11 EVA_UK10K_TWINSUK ss1655887211 Apr 01, 2015 (144)
12 EVA_SVP ss1712763964 Apr 01, 2015 (144)
13 HUMAN_LONGEVITY ss2273710203 Dec 20, 2016 (150)
14 GNOMAD ss2824623648 Nov 08, 2017 (151)
15 SWEGEN ss2996935857 Nov 08, 2017 (151)
16 KHV_HUMAN_GENOMES ss3806605585 Jul 13, 2019 (153)
17 EVA ss3829244696 Apr 26, 2020 (154)
18 SGDP_PRJ ss3861858973 Apr 26, 2020 (154)
19 TOPMED ss4660006983 Apr 26, 2021 (155)
20 1000G_HIGH_COVERAGE ss5263979966 Oct 13, 2022 (156)
21 EVA ss5357579844 Oct 13, 2022 (156)
22 HUGCELL_USP ss5462162139 Oct 13, 2022 (156)
23 1000G_HIGH_COVERAGE ss5547635084 Oct 13, 2022 (156)
24 SANFORD_IMAGENETICS ss5637808163 Oct 13, 2022 (156)
25 EVA ss5894192971 Oct 13, 2022 (156)
26 EVA ss5966231641 Oct 13, 2022 (156)
27 1000Genomes NC_000005.9 - 54406950 Oct 12, 2018 (152)
28 1000Genomes_30x NC_000005.10 - 55111122 Oct 13, 2022 (156)
29 The Avon Longitudinal Study of Parents and Children NC_000005.9 - 54406950 Oct 12, 2018 (152)
30 Chileans NC_000005.9 - 54406950 Apr 26, 2020 (154)
31 gnomAD - Genomes NC_000005.10 - 55111122 Apr 26, 2021 (155)
32 SGDP_PRJ NC_000005.9 - 54406950 Apr 26, 2020 (154)
33 TopMed NC_000005.10 - 55111122 Apr 26, 2021 (155)
34 UK 10K study - Twins NC_000005.9 - 54406950 Oct 12, 2018 (152)
35 ALFA NC_000005.10 - 55111122 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).

Associated ID History Updated (Build)
rs61721191 Feb 27, 2009 (130)
rs111033853 Aug 21, 2014 (142)
Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
ss75924946, ss164941108, ss169200004, ss1712763964 NC_000005.8:54442706:A:G NC_000005.10:55111121:A:G (self)
26706893, 14844992, 345892, 13875953, 14844992, ss221679943, ss558392275, ss1315107329, ss1612893178, ss1655887211, ss2824623648, ss2996935857, ss3829244696, ss3861858973, ss5357579844, ss5637808163, ss5966231641 NC_000005.9:54406949:A:G NC_000005.10:55111121:A:G (self)
35161019, 188711316, 497384540, 9811483229, ss2273710203, ss3806605585, ss4660006983, ss5263979966, ss5462162139, ss5547635084, ss5894192971 NC_000005.10:55111121:A:G NC_000005.10:55111121:A:G (self)
ss23349458, ss83236396 NT_006713.15:5001308:A:G NC_000005.10:55111121:A:G (self)
ss66036210 NT_034772.7:5001314:A:G NC_000005.10:55111121:A: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 rs17325399

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