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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.

rs10916825

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr1:20605281 (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>C / A>G / A>T
Variation Type
SNV Single Nucleotide Variation
Frequency
G=0.333700 (88327/264690, TOPMED)
G=0.347183 (48473/139618, GnomAD)
G=0.33215 (15753/47428, ALFA) (+ 16 more)
G=0.33258 (9398/28258, 14KJPN)
G=0.33765 (5659/16760, 8.3KJPN)
G=0.3406 (2181/6404, 1000G_30x)
G=0.3460 (1733/5008, 1000G)
G=0.4658 (2087/4480, Estonian)
G=0.3980 (1534/3854, ALSPAC)
G=0.3746 (1389/3708, TWINSUK)
G=0.3567 (1045/2930, KOREAN)
G=0.3251 (615/1892, HapMap)
G=0.381 (380/998, GoNL)
G=0.427 (256/600, NorthernSweden)
A=0.375 (114/304, SGDP_PRJ)
G=0.389 (84/216, Qatari)
G=0.327 (68/208, Vietnamese)
G=0.28 (11/40, GENOME_DK)
A=0.35 (14/40, Siberian)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
CDA : 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 47428 A=0.66785 C=0.00000, G=0.33215, T=0.00000
European Sub 33708 A=0.64115 C=0.00000, G=0.35885, T=0.00000
African Sub 4840 A=0.8335 C=0.0000, G=0.1665, T=0.0000
African Others Sub 158 A=0.810 C=0.000, G=0.190, T=0.000
African American Sub 4682 A=0.8343 C=0.0000, G=0.1657, T=0.0000
Asian Sub 392 A=0.702 C=0.000, G=0.298, T=0.000
East Asian Sub 328 A=0.686 C=0.000, G=0.314, T=0.000
Other Asian Sub 64 A=0.78 C=0.00, G=0.22, T=0.00
Latin American 1 Sub 500 A=0.660 C=0.000, G=0.340, T=0.000
Latin American 2 Sub 4550 A=0.6956 C=0.0000, G=0.3044, T=0.0000
South Asian Sub 104 A=0.692 C=0.000, G=0.308, T=0.000
Other Sub 3334 A=0.6560 C=0.0000, G=0.3440, T=0.0000


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=0.666300 G=0.333700
gnomAD - Genomes Global Study-wide 139618 A=0.652817 G=0.347183
gnomAD - Genomes European Sub 75654 A=0.59621 G=0.40379
gnomAD - Genomes African Sub 41816 A=0.74634 G=0.25366
gnomAD - Genomes American Sub 13580 A=0.69396 G=0.30604
gnomAD - Genomes Ashkenazi Jewish Sub 3320 A=0.6078 G=0.3922
gnomAD - Genomes East Asian Sub 3112 A=0.6388 G=0.3612
gnomAD - Genomes Other Sub 2136 A=0.6554 G=0.3446
Allele Frequency Aggregator Total Global 47428 A=0.66785 C=0.00000, G=0.33215, T=0.00000
Allele Frequency Aggregator European Sub 33708 A=0.64115 C=0.00000, G=0.35885, T=0.00000
Allele Frequency Aggregator African Sub 4840 A=0.8335 C=0.0000, G=0.1665, T=0.0000
Allele Frequency Aggregator Latin American 2 Sub 4550 A=0.6956 C=0.0000, G=0.3044, T=0.0000
Allele Frequency Aggregator Other Sub 3334 A=0.6560 C=0.0000, G=0.3440, T=0.0000
Allele Frequency Aggregator Latin American 1 Sub 500 A=0.660 C=0.000, G=0.340, T=0.000
Allele Frequency Aggregator Asian Sub 392 A=0.702 C=0.000, G=0.298, T=0.000
Allele Frequency Aggregator South Asian Sub 104 A=0.692 C=0.000, G=0.308, T=0.000
14KJPN JAPANESE Study-wide 28258 A=0.66742 G=0.33258
8.3KJPN JAPANESE Study-wide 16760 A=0.66235 G=0.33765
1000Genomes_30x Global Study-wide 6404 A=0.6594 G=0.3406
1000Genomes_30x African Sub 1786 A=0.7699 G=0.2301
1000Genomes_30x Europe Sub 1266 A=0.6090 G=0.3910
1000Genomes_30x South Asian Sub 1202 A=0.5391 G=0.4609
1000Genomes_30x East Asian Sub 1170 A=0.6402 G=0.3598
1000Genomes_30x American Sub 980 A=0.694 G=0.306
1000Genomes Global Study-wide 5008 A=0.6540 G=0.3460
1000Genomes African Sub 1322 A=0.7663 G=0.2337
1000Genomes East Asian Sub 1008 A=0.6448 G=0.3552
1000Genomes Europe Sub 1006 A=0.6123 G=0.3877
1000Genomes South Asian Sub 978 A=0.519 G=0.481
1000Genomes American Sub 694 A=0.703 G=0.297
Genetic variation in the Estonian population Estonian Study-wide 4480 A=0.5342 G=0.4658
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 A=0.6020 G=0.3980
UK 10K study - Twins TWIN COHORT Study-wide 3708 A=0.6254 G=0.3746
KOREAN population from KRGDB KOREAN Study-wide 2930 A=0.6433 G=0.3567, T=0.0000
HapMap Global Study-wide 1892 A=0.6749 G=0.3251
HapMap American Sub 770 A=0.617 G=0.383
HapMap African Sub 692 A=0.744 G=0.256
HapMap Asian Sub 254 A=0.673 G=0.327
HapMap Europe Sub 176 A=0.659 G=0.341
Genome of the Netherlands Release 5 Genome of the Netherlands Study-wide 998 A=0.619 G=0.381
Northern Sweden ACPOP Study-wide 600 A=0.573 G=0.427
SGDP_PRJ Global Study-wide 304 A=0.375 G=0.625
Qatari Global Study-wide 216 A=0.611 G=0.389
A Vietnamese Genetic Variation Database Global Study-wide 208 A=0.673 G=0.327
The Danish reference pan genome Danish Study-wide 40 A=0.72 G=0.28
Siberian Global Study-wide 40 A=0.35 G=0.65
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 1 NC_000001.11:g.20605281A>C
GRCh38.p14 chr 1 NC_000001.11:g.20605281A>G
GRCh38.p14 chr 1 NC_000001.11:g.20605281A>T
GRCh37.p13 chr 1 NC_000001.10:g.20931774A>C
GRCh37.p13 chr 1 NC_000001.10:g.20931774A>G
GRCh37.p13 chr 1 NC_000001.10:g.20931774A>T
Gene: CDA, cytidine deaminase (plus strand)
Molecule type Change Amino acid[Codon] SO Term
CDA transcript NM_001785.3:c.266+242A>C N/A Intron 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 A= C G T
GRCh38.p14 chr 1 NC_000001.11:g.20605281= NC_000001.11:g.20605281A>C NC_000001.11:g.20605281A>G NC_000001.11:g.20605281A>T
GRCh37.p13 chr 1 NC_000001.10:g.20931774= NC_000001.10:g.20931774A>C NC_000001.10:g.20931774A>G NC_000001.10:g.20931774A>T
CDA transcript NM_001785.2:c.266+242= NM_001785.2:c.266+242A>C NM_001785.2:c.266+242A>G NM_001785.2:c.266+242A>T
CDA transcript NM_001785.3:c.266+242= NM_001785.3:c.266+242A>C NM_001785.3:c.266+242A>G NM_001785.3:c.266+242A>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#.

74 SubSNP, 19 Frequency submissions
No Submitter Submission ID Date (Build)
1 CSHL-HAPMAP ss17331392 Feb 27, 2004 (120)
2 SC_SNP ss18146231 Feb 27, 2004 (120)
3 ILLUMINA ss75267644 Dec 07, 2007 (129)
4 SI_EXO ss76887642 Dec 07, 2007 (129)
5 BCMHGSC_JDW ss87282995 Mar 23, 2008 (129)
6 BGI ss102725793 Dec 01, 2009 (131)
7 1000GENOMES ss108047015 Jan 22, 2009 (130)
8 KRIBB_YJKIM ss119650722 Dec 01, 2009 (131)
9 ENSEMBL ss131741090 Dec 01, 2009 (131)
10 ENSEMBL ss137834193 Dec 01, 2009 (131)
11 ILLUMINA ss159938161 Dec 01, 2009 (131)
12 COMPLETE_GENOMICS ss166207528 Jul 04, 2010 (132)
13 ILLUMINA ss170748873 Jul 04, 2010 (132)
14 BUSHMAN ss198135477 Jul 04, 2010 (132)
15 BCM-HGSC-SUB ss205359740 Jul 04, 2010 (132)
16 1000GENOMES ss210483583 Jul 14, 2010 (132)
17 1000GENOMES ss218273586 Jul 14, 2010 (132)
18 1000GENOMES ss230454748 Jul 14, 2010 (132)
19 1000GENOMES ss238164361 Jul 15, 2010 (132)
20 BL ss252968103 May 09, 2011 (134)
21 GMI ss275745407 May 04, 2012 (137)
22 GMI ss284014850 Apr 25, 2013 (138)
23 ILLUMINA ss479818717 Sep 08, 2015 (146)
24 ILLUMINA ss536652846 Sep 08, 2015 (146)
25 TISHKOFF ss553870312 Apr 25, 2013 (138)
26 SSMP ss647627022 Apr 25, 2013 (138)
27 EVA-GONL ss974926288 Aug 21, 2014 (142)
28 1000GENOMES ss1289958568 Aug 21, 2014 (142)
29 DDI ss1425738836 Apr 01, 2015 (144)
30 EVA_GENOME_DK ss1573928953 Apr 01, 2015 (144)
31 EVA_UK10K_ALSPAC ss1599687155 Apr 01, 2015 (144)
32 EVA_UK10K_TWINSUK ss1642681188 Apr 01, 2015 (144)
33 EVA_SVP ss1712316526 Apr 01, 2015 (144)
34 WEILL_CORNELL_DGM ss1918138037 Feb 12, 2016 (147)
35 JJLAB ss2019580791 Sep 14, 2016 (149)
36 USC_VALOUEV ss2147584409 Dec 20, 2016 (150)
37 HUMAN_LONGEVITY ss2160567475 Dec 20, 2016 (150)
38 SYSTEMSBIOZJU ss2624306752 Nov 08, 2017 (151)
39 GRF ss2697488942 Nov 08, 2017 (151)
40 GNOMAD ss2752441093 Nov 08, 2017 (151)
41 SWEGEN ss2986433075 Nov 08, 2017 (151)
42 BIOINF_KMB_FNS_UNIBA ss3023555660 Nov 08, 2017 (151)
43 CSHL ss3343357866 Nov 08, 2017 (151)
44 ILLUMINA ss3626043623 Oct 11, 2018 (152)
45 ILLUMINA ss3635987586 Oct 11, 2018 (152)
46 ILLUMINA ss3637741758 Oct 11, 2018 (152)
47 ILLUMINA ss3642755209 Oct 11, 2018 (152)
48 URBANLAB ss3646617434 Oct 11, 2018 (152)
49 EGCUT_WGS ss3654503536 Jul 12, 2019 (153)
50 EVA_DECODE ss3686305331 Jul 12, 2019 (153)
51 ACPOP ss3726852230 Jul 12, 2019 (153)
52 EVA ss3745916995 Jul 12, 2019 (153)
53 KHV_HUMAN_GENOMES ss3798936757 Jul 12, 2019 (153)
54 EVA ss3826060551 Apr 25, 2020 (154)
55 EVA ss3836418479 Apr 25, 2020 (154)
56 EVA ss3841822927 Apr 25, 2020 (154)
57 SGDP_PRJ ss3848364398 Apr 25, 2020 (154)
58 KRGDB ss3893273198 Apr 25, 2020 (154)
59 EVA ss4016897204 Apr 27, 2021 (155)
60 TOPMED ss4441462691 Apr 27, 2021 (155)
61 TOMMO_GENOMICS ss5142834038 Apr 27, 2021 (155)
62 1000G_HIGH_COVERAGE ss5241438351 Oct 19, 2022 (156)
63 EVA ss5317210089 Oct 19, 2022 (156)
64 HUGCELL_USP ss5442596170 Oct 19, 2022 (156)
65 EVA ss5505783711 Oct 19, 2022 (156)
66 1000G_HIGH_COVERAGE ss5513313885 Oct 19, 2022 (156)
67 EVA ss5623989264 Oct 19, 2022 (156)
68 SANFORD_IMAGENETICS ss5625073684 Oct 19, 2022 (156)
69 TOMMO_GENOMICS ss5667241283 Oct 19, 2022 (156)
70 YY_MCH ss5800394624 Oct 19, 2022 (156)
71 EVA ss5831641080 Oct 19, 2022 (156)
72 EVA ss5848814899 Oct 19, 2022 (156)
73 EVA ss5907317738 Oct 19, 2022 (156)
74 EVA ss5936889511 Oct 19, 2022 (156)
75 1000Genomes NC_000001.10 - 20931774 Oct 11, 2018 (152)
76 1000Genomes_30x NC_000001.11 - 20605281 Oct 19, 2022 (156)
77 The Avon Longitudinal Study of Parents and Children NC_000001.10 - 20931774 Oct 11, 2018 (152)
78 Genetic variation in the Estonian population NC_000001.10 - 20931774 Oct 11, 2018 (152)
79 The Danish reference pan genome NC_000001.10 - 20931774 Apr 25, 2020 (154)
80 gnomAD - Genomes NC_000001.11 - 20605281 Apr 27, 2021 (155)
81 Genome of the Netherlands Release 5 NC_000001.10 - 20931774 Apr 25, 2020 (154)
82 HapMap NC_000001.11 - 20605281 Apr 25, 2020 (154)
83 KOREAN population from KRGDB NC_000001.10 - 20931774 Apr 25, 2020 (154)
84 Northern Sweden NC_000001.10 - 20931774 Jul 12, 2019 (153)
85 Qatari NC_000001.10 - 20931774 Apr 25, 2020 (154)
86 SGDP_PRJ NC_000001.10 - 20931774 Apr 25, 2020 (154)
87 Siberian NC_000001.10 - 20931774 Apr 25, 2020 (154)
88 8.3KJPN NC_000001.10 - 20931774 Apr 27, 2021 (155)
89 14KJPN NC_000001.11 - 20605281 Oct 19, 2022 (156)
90 TopMed NC_000001.11 - 20605281 Apr 27, 2021 (155)
91 UK 10K study - Twins NC_000001.10 - 20931774 Oct 11, 2018 (152)
92 A Vietnamese Genetic Variation Database NC_000001.10 - 20931774 Jul 12, 2019 (153)
93 ALFA NC_000001.11 - 20605281 Apr 27, 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
2834412840 NC_000001.11:20605280:A:C NC_000001.11:20605280:A:C (self)
ss87282995, ss108047015, ss159938161, ss166207528, ss198135477, ss205359740, ss210483583, ss252968103, ss275745407, ss284014850, ss1712316526, ss3642755209 NC_000001.9:20804360:A:G NC_000001.11:20605280:A:G (self)
643786, 339538, 241784, 1418206, 147501, 450592, 137095, 179967, 381378, 100763, 803345, 339538, 72778, ss218273586, ss230454748, ss238164361, ss479818717, ss536652846, ss553870312, ss647627022, ss974926288, ss1289958568, ss1425738836, ss1573928953, ss1599687155, ss1642681188, ss1918138037, ss2019580791, ss2147584409, ss2624306752, ss2697488942, ss2752441093, ss2986433075, ss3343357866, ss3626043623, ss3635987586, ss3637741758, ss3654503536, ss3726852230, ss3745916995, ss3826060551, ss3836418479, ss3848364398, ss3893273198, ss4016897204, ss5142834038, ss5317210089, ss5505783711, ss5623989264, ss5625073684, ss5831641080, ss5936889511 NC_000001.10:20931773:A:G NC_000001.11:20605280:A:G (self)
839820, 4468239, 26583, 1078387, 5069026, 2834412840, ss2160567475, ss3023555660, ss3646617434, ss3686305331, ss3798936757, ss3841822927, ss4441462691, ss5241438351, ss5442596170, ss5513313885, ss5667241283, ss5800394624, ss5848814899, ss5907317738 NC_000001.11:20605280:A:G NC_000001.11:20605280:A:G (self)
ss17331392, ss18146231 NT_004610.16:1735023:A:G NC_000001.11:20605280:A:G (self)
ss76887642 NT_004610.18:3756115:A:G NC_000001.11:20605280:A:G (self)
ss75267644, ss102725793, ss119650722, ss131741090, ss137834193, ss170748873 NT_004610.19:7611861:A:G NC_000001.11:20605280:A:G (self)
450592, ss3893273198 NC_000001.10:20931773:A:T NC_000001.11:20605280:A:T (self)
2834412840 NC_000001.11:20605280:A:T NC_000001.11:20605280:A: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 rs10916825

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