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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.

rs76921025

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr17:40318413 (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=0.010461 (2769/264690, TOPMED)
G=0.009679 (1358/140308, GnomAD)
G=0.01047 (210/20054, ALFA) (+ 9 more)
G=0.0061 (39/6404, 1000G_30x)
G=0.0048 (24/5008, 1000G)
G=0.0056 (25/4480, Estonian)
G=0.0125 (48/3854, ALSPAC)
G=0.0113 (42/3708, TWINSUK)
G=0.012 (7/600, NorthernSweden)
G=0.037 (8/216, Qatari)
C=0.50 (8/16, SGDP_PRJ)
G=0.50 (8/16, SGDP_PRJ)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
RARA : Intron 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 20054 C=0.98953 G=0.01047
European Sub 15424 C=0.98788 G=0.01212
African Sub 2946 C=0.9969 G=0.0031
African Others Sub 114 C=1.000 G=0.000
African American Sub 2832 C=0.9968 G=0.0032
Asian Sub 112 C=1.000 G=0.000
East Asian Sub 86 C=1.00 G=0.00
Other Asian Sub 26 C=1.00 G=0.00
Latin American 1 Sub 146 C=0.993 G=0.007
Latin American 2 Sub 610 C=0.995 G=0.005
South Asian Sub 98 C=1.00 G=0.00
Other Sub 718 C=0.986 G=0.014


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 C=0.989539 G=0.010461
gnomAD - Genomes Global Study-wide 140308 C=0.990321 G=0.009679
gnomAD - Genomes European Sub 75964 C=0.98773 G=0.01227
gnomAD - Genomes African Sub 42066 C=0.99717 G=0.00283
gnomAD - Genomes American Sub 13668 C=0.98581 G=0.01419
gnomAD - Genomes Ashkenazi Jewish Sub 3322 C=0.9741 G=0.0259
gnomAD - Genomes East Asian Sub 3134 C=0.9997 G=0.0003
gnomAD - Genomes Other Sub 2154 C=0.9879 G=0.0121
Allele Frequency Aggregator Total Global 20054 C=0.98953 G=0.01047
Allele Frequency Aggregator European Sub 15424 C=0.98788 G=0.01212
Allele Frequency Aggregator African Sub 2946 C=0.9969 G=0.0031
Allele Frequency Aggregator Other Sub 718 C=0.986 G=0.014
Allele Frequency Aggregator Latin American 2 Sub 610 C=0.995 G=0.005
Allele Frequency Aggregator Latin American 1 Sub 146 C=0.993 G=0.007
Allele Frequency Aggregator Asian Sub 112 C=1.000 G=0.000
Allele Frequency Aggregator South Asian Sub 98 C=1.00 G=0.00
1000Genomes_30x Global Study-wide 6404 C=0.9939 G=0.0061
1000Genomes_30x African Sub 1786 C=1.0000 G=0.0000
1000Genomes_30x Europe Sub 1266 C=0.9771 G=0.0229
1000Genomes_30x South Asian Sub 1202 C=0.9967 G=0.0033
1000Genomes_30x East Asian Sub 1170 C=1.0000 G=0.0000
1000Genomes_30x American Sub 980 C=0.994 G=0.006
1000Genomes Global Study-wide 5008 C=0.9952 G=0.0048
1000Genomes African Sub 1322 C=1.0000 G=0.0000
1000Genomes East Asian Sub 1008 C=1.0000 G=0.0000
1000Genomes Europe Sub 1006 C=0.9841 G=0.0159
1000Genomes South Asian Sub 978 C=0.996 G=0.004
1000Genomes American Sub 694 C=0.994 G=0.006
Genetic variation in the Estonian population Estonian Study-wide 4480 C=0.9944 G=0.0056
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 C=0.9875 G=0.0125
UK 10K study - Twins TWIN COHORT Study-wide 3708 C=0.9887 G=0.0113
Northern Sweden ACPOP Study-wide 600 C=0.988 G=0.012
Qatari Global Study-wide 216 C=0.963 G=0.037
SGDP_PRJ Global Study-wide 16 C=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 17 NC_000017.11:g.40318413C>G
GRCh37.p13 chr 17 NC_000017.10:g.38474665C>G
RARA RefSeqGene (LRG_1070) NG_027701.1:g.14243C>G
Gene: RARA, retinoic acid receptor alpha (plus strand)
Molecule type Change Amino acid[Codon] SO Term
RARA transcript variant 1 NM_000964.4:c.-363+9127C>G N/A Intron Variant
RARA transcript variant 3 NM_001145301.3:c.-398= N/A 5 Prime UTR Variant
RARA transcript variant 4 NM_001145302.3:c.-398= N/A 5 Prime UTR Variant
RARA transcript variant 2 NM_001024809.4:c. N/A Genic Upstream Transcript Variant
RARA transcript variant X2 XM_011525095.2:c.-439-806…

XM_011525095.2:c.-439-8062C>G

N/A Intron Variant
RARA transcript variant X5 XM_005257552.6:c. N/A Genic Upstream Transcript Variant
RARA transcript variant X4 XM_005257553.2:c. N/A Genic Upstream Transcript Variant
RARA transcript variant X3 XM_005257554.2:c. N/A Genic Upstream Transcript Variant
RARA transcript variant X8 XM_011525096.2:c. N/A Genic Upstream Transcript Variant
RARA transcript variant X1 XM_047436506.1:c. N/A Genic Upstream Transcript Variant
RARA transcript variant X6 XM_047436507.1:c. N/A Genic Upstream Transcript Variant
RARA transcript variant X7 XM_047436508.1:c. N/A Genic 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

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 17 NC_000017.11:g.40318413= NC_000017.11:g.40318413C>G
GRCh37.p13 chr 17 NC_000017.10:g.38474665= NC_000017.10:g.38474665C>G
RARA RefSeqGene (LRG_1070) NG_027701.1:g.14243= NG_027701.1:g.14243C>G
RARA transcript variant 3 NM_001145301.3:c.-398= NM_001145301.3:c.-398C>G
RARA transcript variant 3 NM_001145301.2:c.-398= NM_001145301.2:c.-398C>G
RARA transcript variant 4 NM_001145302.3:c.-398= NM_001145302.3:c.-398C>G
RARA transcript variant 4 NM_001145302.2:c.-398= NM_001145302.2:c.-398C>G
RARA transcript NM_001033603.1:c.-398= NM_001033603.1:c.-398C>G
RARA transcript variant 1 NM_000964.3:c.-363+9127= NM_000964.3:c.-363+9127C>G
RARA transcript variant 1 NM_000964.4:c.-363+9127= NM_000964.4:c.-363+9127C>G
RARA transcript variant X2 XM_011525095.2:c.-439-8062= XM_011525095.2:c.-439-8062C>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, 11 Frequency submissions
No Submitter Submission ID Date (Build)
1 ILLUMINA ss159849030 Dec 01, 2009 (131)
2 ILLUMINA ss168973928 Jul 04, 2010 (132)
3 BUSHMAN ss202498862 Jul 04, 2010 (132)
4 1000GENOMES ss237239346 Jul 15, 2010 (132)
5 ILLUMINA ss479156196 Sep 08, 2015 (146)
6 EVA-GONL ss993093540 Aug 21, 2014 (142)
7 1000GENOMES ss1358594238 Aug 21, 2014 (142)
8 EVA_UK10K_ALSPAC ss1635622804 Apr 01, 2015 (144)
9 EVA_UK10K_TWINSUK ss1678616837 Apr 01, 2015 (144)
10 EVA_DECODE ss1697135702 Apr 01, 2015 (144)
11 WEILL_CORNELL_DGM ss1936552947 Feb 12, 2016 (147)
12 HUMAN_LONGEVITY ss2216725068 Dec 20, 2016 (150)
13 GNOMAD ss2949697079 Nov 08, 2017 (151)
14 SWEGEN ss3015509348 Nov 08, 2017 (151)
15 ILLUMINA ss3636364236 Oct 12, 2018 (152)
16 ILLUMINA ss3638160274 Oct 12, 2018 (152)
17 EGCUT_WGS ss3682400176 Jul 13, 2019 (153)
18 EVA_DECODE ss3700436373 Jul 13, 2019 (153)
19 ACPOP ss3742013868 Jul 13, 2019 (153)
20 EVA ss3754649498 Jul 13, 2019 (153)
21 SGDP_PRJ ss3885719554 Apr 27, 2020 (154)
22 TOPMED ss5035464102 Apr 26, 2021 (155)
23 1000G_HIGH_COVERAGE ss5303080028 Oct 16, 2022 (156)
24 EVA ss5427500248 Oct 16, 2022 (156)
25 HUGCELL_USP ss5496142916 Oct 16, 2022 (156)
26 1000G_HIGH_COVERAGE ss5606774814 Oct 16, 2022 (156)
27 SANFORD_IMAGENETICS ss5660074089 Oct 16, 2022 (156)
28 EVA ss5833962804 Oct 16, 2022 (156)
29 EVA ss5913899035 Oct 16, 2022 (156)
30 EVA ss5951467580 Oct 16, 2022 (156)
31 1000Genomes NC_000017.10 - 38474665 Oct 12, 2018 (152)
32 1000Genomes_30x NC_000017.11 - 40318413 Oct 16, 2022 (156)
33 The Avon Longitudinal Study of Parents and Children NC_000017.10 - 38474665 Oct 12, 2018 (152)
34 Genetic variation in the Estonian population NC_000017.10 - 38474665 Oct 12, 2018 (152)
35 gnomAD - Genomes NC_000017.11 - 40318413 Apr 26, 2021 (155)
36 Northern Sweden NC_000017.10 - 38474665 Jul 13, 2019 (153)
37 Qatari NC_000017.10 - 38474665 Apr 27, 2020 (154)
38 SGDP_PRJ NC_000017.10 - 38474665 Apr 27, 2020 (154)
39 TopMed NC_000017.11 - 40318413 Apr 26, 2021 (155)
40 UK 10K study - Twins NC_000017.10 - 38474665 Oct 12, 2018 (152)
41 ALFA NC_000017.11 - 40318413 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
ss159849030, ss202498862, ss1697135702 NC_000017.9:35728190:C:G NC_000017.11:40318412:C:G (self)
71833793, 39815253, 28138424, 15298733, 18594869, 37736534, 39815253, ss237239346, ss479156196, ss993093540, ss1358594238, ss1635622804, ss1678616837, ss1936552947, ss2949697079, ss3015509348, ss3636364236, ss3638160274, ss3682400176, ss3742013868, ss3754649498, ss3885719554, ss5427500248, ss5660074089, ss5833962804, ss5951467580 NC_000017.10:38474664:C:G NC_000017.11:40318412:C:G (self)
94300749, 506802555, 251009764, 10217477784, ss2216725068, ss3700436373, ss5035464102, ss5303080028, ss5496142916, ss5606774814, ss5913899035 NC_000017.11:40318412:C:G NC_000017.11:40318412:C:G (self)
ss168973928 NT_010783.15:3748816:C:G NC_000017.11:40318412: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 rs76921025

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