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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.

rs28432925

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr17:200158 (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
G>A / G>C
Variation Type
SNV Single Nucleotide Variation
Frequency
A=0.086180 (22811/264690, TOPMED)
A=0.081998 (11490/140126, GnomAD)
A=0.00004 (1/28258, 14KJPN) (+ 10 more)
A=0.00006 (1/16760, 8.3KJPN)
A=0.01381 (182/13176, ALFA)
A=0.0878 (562/6404, 1000G_30x)
A=0.0817 (409/5008, 1000G)
A=0.0008 (3/3854, ALSPAC)
A=0.0000 (0/3708, TWINSUK)
A=0.0003 (1/2922, KOREAN)
A=0.042 (9/216, Qatari)
G=0.50 (23/46, SGDP_PRJ)
A=0.50 (23/46, SGDP_PRJ)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
LOC101929045 : Non Coding Transcript Variant
LOC124903889 : 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 13176 G=0.98619 A=0.01381, C=0.00000
European Sub 9804 G=0.9991 A=0.0009, C=0.0000
African Sub 1840 G=0.9103 A=0.0897, C=0.0000
African Others Sub 66 G=0.86 A=0.14, C=0.00
African American Sub 1774 G=0.9121 A=0.0879, C=0.0000
Asian Sub 112 G=1.000 A=0.000, C=0.000
East Asian Sub 86 G=1.00 A=0.00, C=0.00
Other Asian Sub 26 G=1.00 A=0.00, C=0.00
Latin American 1 Sub 126 G=1.000 A=0.000, C=0.000
Latin American 2 Sub 580 G=1.000 A=0.000, C=0.000
South Asian Sub 98 G=1.00 A=0.00, C=0.00
Other Sub 616 G=0.987 A=0.013, C=0.000


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 G=0.913820 A=0.086180
gnomAD - Genomes Global Study-wide 140126 G=0.918002 A=0.081998
gnomAD - Genomes European Sub 75932 G=0.99879 A=0.00121
gnomAD - Genomes African Sub 41944 G=0.74111 A=0.25889
gnomAD - Genomes American Sub 13646 G=0.96988 A=0.03012
gnomAD - Genomes Ashkenazi Jewish Sub 3322 G=0.9994 A=0.0006
gnomAD - Genomes East Asian Sub 3132 G=1.0000 A=0.0000
gnomAD - Genomes Other Sub 2150 G=0.9414 A=0.0586
14KJPN JAPANESE Study-wide 28258 G=0.99996 A=0.00004
8.3KJPN JAPANESE Study-wide 16760 G=0.99994 A=0.00006
Allele Frequency Aggregator Total Global 13176 G=0.98619 A=0.01381, C=0.00000
Allele Frequency Aggregator European Sub 9804 G=0.9991 A=0.0009, C=0.0000
Allele Frequency Aggregator African Sub 1840 G=0.9103 A=0.0897, C=0.0000
Allele Frequency Aggregator Other Sub 616 G=0.987 A=0.013, C=0.000
Allele Frequency Aggregator Latin American 2 Sub 580 G=1.000 A=0.000, C=0.000
Allele Frequency Aggregator Latin American 1 Sub 126 G=1.000 A=0.000, C=0.000
Allele Frequency Aggregator Asian Sub 112 G=1.000 A=0.000, C=0.000
Allele Frequency Aggregator South Asian Sub 98 G=1.00 A=0.00, C=0.00
1000Genomes_30x Global Study-wide 6404 G=0.9122 A=0.0878
1000Genomes_30x African Sub 1786 G=0.6960 A=0.3040
1000Genomes_30x Europe Sub 1266 G=0.9968 A=0.0032
1000Genomes_30x South Asian Sub 1202 G=1.0000 A=0.0000
1000Genomes_30x East Asian Sub 1170 G=1.0000 A=0.0000
1000Genomes_30x American Sub 980 G=0.985 A=0.015
1000Genomes Global Study-wide 5008 G=0.9183 A=0.0817
1000Genomes African Sub 1322 G=0.7012 A=0.2988
1000Genomes East Asian Sub 1008 G=1.0000 A=0.0000
1000Genomes Europe Sub 1006 G=0.9980 A=0.0020
1000Genomes South Asian Sub 978 G=1.000 A=0.000
1000Genomes American Sub 694 G=0.983 A=0.017
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 G=0.9992 A=0.0008
UK 10K study - Twins TWIN COHORT Study-wide 3708 G=1.0000 A=0.0000
KOREAN population from KRGDB KOREAN Study-wide 2922 G=0.9997 A=0.0003
Qatari Global Study-wide 216 G=0.958 A=0.042
SGDP_PRJ Global Study-wide 46 G=0.50 A=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 17 NC_000017.11:g.200158G>A
GRCh38.p14 chr 17 NC_000017.11:g.200158G>C
GRCh37.p13 chr 17 fix patch HG417_PATCH NW_004070872.2:g.140156G>A
GRCh37.p13 chr 17 fix patch HG417_PATCH NW_004070872.2:g.140156G>C
GRCh38.p14 chr 17 alt locus HSCHR17_1_CTG1 NW_003315952.3:g.139213G>A
GRCh38.p14 chr 17 alt locus HSCHR17_1_CTG1 NW_003315952.3:g.139213G>C
GRCh37.p13 chr 17 NC_000017.10:g.49949G>A
GRCh37.p13 chr 17 NC_000017.10:g.49949G>C
Gene: LOC124903889, uncharacterized LOC124903889 (minus strand)
Molecule type Change Amino acid[Codon] SO Term
LOC124903889 transcript XR_007065569.1:n.173C>T N/A Non Coding Transcript Variant
LOC124903889 transcript XR_007065569.1:n.173C>G N/A Non Coding 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

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 G= A C
GRCh38.p14 chr 17 NC_000017.11:g.200158= NC_000017.11:g.200158G>A NC_000017.11:g.200158G>C
GRCh37.p13 chr 17 fix patch HG417_PATCH NW_004070872.2:g.140156= NW_004070872.2:g.140156G>A NW_004070872.2:g.140156G>C
GRCh38.p14 chr 17 alt locus HSCHR17_1_CTG1 NW_003315952.3:g.139213= NW_003315952.3:g.139213G>A NW_003315952.3:g.139213G>C
GRCh37.p13 chr 17 NC_000017.10:g.49949= NC_000017.10:g.49949G>A NC_000017.10:g.49949G>C
LOC101929045 transcript XR_952137.3:n.4690= XR_952137.3:n.4690C>T XR_952137.3:n.4690C>G
LOC101929045 transcript XR_952137.2:n.4146= XR_952137.2:n.4146C>T XR_952137.2:n.4146C>G
LOC101929045 transcript XR_952137.1:n.2750= XR_952137.1:n.2750C>T XR_952137.1:n.2750C>G
LOC124903889 transcript XR_007065569.1:n.173= XR_007065569.1:n.173C>T XR_007065569.1:n.173C>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#.

30 SubSNP, 12 Frequency submissions
No Submitter Submission ID Date (Build)
1 SSAHASNP ss35149195 May 24, 2005 (125)
2 HGSV ss81283530 Dec 14, 2007 (130)
3 ILLUMINA-UK ss117967094 Feb 14, 2009 (130)
4 BUSHMAN ss202105021 Jul 04, 2010 (132)
5 1000GENOMES ss211763323 Jul 14, 2010 (132)
6 1000GENOMES ss227420405 Jul 14, 2010 (132)
7 TISHKOFF ss565113803 Apr 25, 2013 (138)
8 1000GENOMES ss1357570902 Aug 21, 2014 (142)
9 EVA_UK10K_ALSPAC ss1635121058 Apr 01, 2015 (144)
10 EVA_UK10K_TWINSUK ss1678115091 Apr 01, 2015 (144)
11 HAMMER_LAB ss1808663757 Sep 08, 2015 (146)
12 WEILL_CORNELL_DGM ss1936276248 Feb 12, 2016 (147)
13 HUMAN_LONGEVITY ss2214838979 Dec 20, 2016 (150)
14 GNOMAD ss2946736463 Nov 08, 2017 (151)
15 EVA_DECODE ss3699911170 Jul 13, 2019 (153)
16 KHV_HUMAN_GENOMES ss3819616035 Jul 13, 2019 (153)
17 EVA ss3834733388 Apr 27, 2020 (154)
18 SGDP_PRJ ss3885145510 Apr 27, 2020 (154)
19 KRGDB ss3934712318 Apr 27, 2020 (154)
20 TOPMED ss5026703571 Apr 26, 2021 (155)
21 TOMMO_GENOMICS ss5221082709 Apr 26, 2021 (155)
22 1000G_HIGH_COVERAGE ss5302117342 Oct 17, 2022 (156)
23 EVA ss5425841757 Oct 17, 2022 (156)
24 HUGCELL_USP ss5495335121 Oct 17, 2022 (156)
25 1000G_HIGH_COVERAGE ss5605344637 Oct 17, 2022 (156)
26 SANFORD_IMAGENETICS ss5659551598 Oct 17, 2022 (156)
27 TOMMO_GENOMICS ss5776544272 Oct 17, 2022 (156)
28 EVA ss5833598412 Oct 17, 2022 (156)
29 EVA ss5912897553 Oct 17, 2022 (156)
30 EVA ss5950964408 Oct 17, 2022 (156)
31 1000Genomes NC_000017.10 - 49949 Oct 12, 2018 (152)
32 1000Genomes_30x NC_000017.11 - 200158 Oct 17, 2022 (156)
33 The Avon Longitudinal Study of Parents and Children NC_000017.10 - 49949 Oct 12, 2018 (152)
34 gnomAD - Genomes NC_000017.11 - 200158 Apr 26, 2021 (155)
35 KOREAN population from KRGDB NC_000017.10 - 49949 Apr 27, 2020 (154)
36 Qatari NC_000017.10 - 49949 Apr 27, 2020 (154)
37 SGDP_PRJ NC_000017.10 - 49949 Apr 27, 2020 (154)
38 8.3KJPN NC_000017.10 - 49949 Apr 26, 2021 (155)
39 14KJPN NC_000017.11 - 200158 Oct 17, 2022 (156)
40 TopMed NC_000017.11 - 200158 Apr 26, 2021 (155)
41 UK 10K study - Twins NC_000017.10 - 49949 Oct 12, 2018 (152)
42 ALFA NC_000017.11 - 200158 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)
rs57538935 May 23, 2008 (130)
Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
ss35149195, ss81283530, ss117967094, ss202105021, ss211763323 NC_000017.9:49948:G:A NC_000017.11:200157:G:A (self)
70772462, 39257650, 41889712, 18318170, 37162490, 79052016, 39257650, ss227420405, ss565113803, ss1357570902, ss1635121058, ss1678115091, ss1808663757, ss1936276248, ss2946736463, ss3834733388, ss3885145510, ss3934712318, ss5221082709, ss5425841757, ss5659551598, ss5833598412, ss5950964408 NC_000017.10:49948:G:A NC_000017.11:200157:G:A (self)
92870572, 499077819, 110381376, 242249233, 9062053381, ss2214838979, ss3699911170, ss3819616035, ss5026703571, ss5302117342, ss5495335121, ss5605344637, ss5776544272, ss5912897553 NC_000017.11:200157:G:A NC_000017.11:200157:G:A (self)
9062053381 NC_000017.11:200157:G:C NC_000017.11:200157:G: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 rs28432925

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