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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.

rs13070856

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr3:126190572 (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=0.236817 (62683/264690, TOPMED)
A=0.284552 (42565/149586, ALFA)
A=0.240679 (33711/140066, GnomAD) (+ 18 more)
A=0.21951 (6203/28258, 14KJPN)
A=0.21856 (3663/16760, 8.3KJPN)
A=0.2128 (1363/6404, 1000G_30x)
A=0.2173 (1088/5008, 1000G)
A=0.3283 (1471/4480, Estonian)
A=0.2667 (1028/3854, ALSPAC)
A=0.2721 (1009/3708, TWINSUK)
A=0.2495 (731/2930, KOREAN)
A=0.1755 (331/1886, HapMap)
A=0.2835 (322/1136, Daghestan)
A=0.287 (286/998, GoNL)
A=0.204 (128/626, Chileans)
A=0.307 (184/600, NorthernSweden)
A=0.407 (88/216, Qatari)
A=0.238 (51/214, Vietnamese)
G=0.399 (83/208, SGDP_PRJ)
A=0.25 (10/40, GENOME_DK)
G=0.32 (11/34, Siberian)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
ALDH1L1 : Intron Variant
ALDH1L1-AS2 : 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 149586 G=0.715448 A=0.284552, C=0.000000
European Sub 123832 G=0.696112 A=0.303888, C=0.000000
African Sub 8714 G=0.8815 A=0.1185, C=0.0000
African Others Sub 288 G=0.892 A=0.108, C=0.000
African American Sub 8426 G=0.8811 A=0.1189, C=0.0000
Asian Sub 672 G=0.786 A=0.214, C=0.000
East Asian Sub 508 G=0.776 A=0.224, C=0.000
Other Asian Sub 164 G=0.817 A=0.183, C=0.000
Latin American 1 Sub 884 G=0.725 A=0.275, C=0.000
Latin American 2 Sub 8434 G=0.7981 A=0.2019, C=0.0000
South Asian Sub 198 G=0.813 A=0.187, C=0.000
Other Sub 6852 G=0.7411 A=0.2589, C=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 G=0.763183 A=0.236817
Allele Frequency Aggregator Total Global 149586 G=0.715448 A=0.284552, C=0.000000
Allele Frequency Aggregator European Sub 123832 G=0.696112 A=0.303888, C=0.000000
Allele Frequency Aggregator African Sub 8714 G=0.8815 A=0.1185, C=0.0000
Allele Frequency Aggregator Latin American 2 Sub 8434 G=0.7981 A=0.2019, C=0.0000
Allele Frequency Aggregator Other Sub 6852 G=0.7411 A=0.2589, C=0.0000
Allele Frequency Aggregator Latin American 1 Sub 884 G=0.725 A=0.275, C=0.000
Allele Frequency Aggregator Asian Sub 672 G=0.786 A=0.214, C=0.000
Allele Frequency Aggregator South Asian Sub 198 G=0.813 A=0.187, C=0.000
gnomAD - Genomes Global Study-wide 140066 G=0.759321 A=0.240679
gnomAD - Genomes European Sub 75846 G=0.70303 A=0.29697
gnomAD - Genomes African Sub 41972 G=0.87230 A=0.12770
gnomAD - Genomes American Sub 13654 G=0.75934 A=0.24066
gnomAD - Genomes Ashkenazi Jewish Sub 3322 G=0.6538 A=0.3462
gnomAD - Genomes East Asian Sub 3122 G=0.7489 A=0.2511
gnomAD - Genomes Other Sub 2150 G=0.7177 A=0.2823
14KJPN JAPANESE Study-wide 28258 G=0.78049 A=0.21951
8.3KJPN JAPANESE Study-wide 16760 G=0.78144 A=0.21856
1000Genomes_30x Global Study-wide 6404 G=0.7872 A=0.2128
1000Genomes_30x African Sub 1786 G=0.9087 A=0.0913
1000Genomes_30x Europe Sub 1266 G=0.6935 A=0.3065
1000Genomes_30x South Asian Sub 1202 G=0.7696 A=0.2304
1000Genomes_30x East Asian Sub 1170 G=0.7427 A=0.2573
1000Genomes_30x American Sub 980 G=0.761 A=0.239
1000Genomes Global Study-wide 5008 G=0.7827 A=0.2173
1000Genomes African Sub 1322 G=0.9077 A=0.0923
1000Genomes East Asian Sub 1008 G=0.7381 A=0.2619
1000Genomes Europe Sub 1006 G=0.6849 A=0.3151
1000Genomes South Asian Sub 978 G=0.772 A=0.228
1000Genomes American Sub 694 G=0.767 A=0.233
Genetic variation in the Estonian population Estonian Study-wide 4480 G=0.6717 A=0.3283
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 G=0.7333 A=0.2667
UK 10K study - Twins TWIN COHORT Study-wide 3708 G=0.7279 A=0.2721
KOREAN population from KRGDB KOREAN Study-wide 2930 G=0.7505 A=0.2495
HapMap Global Study-wide 1886 G=0.8245 A=0.1755
HapMap American Sub 768 G=0.805 A=0.195
HapMap African Sub 688 G=0.929 A=0.071
HapMap Asian Sub 254 G=0.717 A=0.283
HapMap Europe Sub 176 G=0.659 A=0.341
Genome-wide autozygosity in Daghestan Global Study-wide 1136 G=0.7165 A=0.2835
Genome-wide autozygosity in Daghestan Daghestan Sub 628 G=0.713 A=0.287
Genome-wide autozygosity in Daghestan Near_East Sub 144 G=0.653 A=0.347
Genome-wide autozygosity in Daghestan Central Asia Sub 122 G=0.787 A=0.213
Genome-wide autozygosity in Daghestan Europe Sub 108 G=0.694 A=0.306
Genome-wide autozygosity in Daghestan South Asian Sub 98 G=0.82 A=0.18
Genome-wide autozygosity in Daghestan Caucasus Sub 36 G=0.58 A=0.42
Genome of the Netherlands Release 5 Genome of the Netherlands Study-wide 998 G=0.713 A=0.287
Chileans Chilean Study-wide 626 G=0.796 A=0.204
Northern Sweden ACPOP Study-wide 600 G=0.693 A=0.307
Qatari Global Study-wide 216 G=0.593 A=0.407
A Vietnamese Genetic Variation Database Global Study-wide 214 G=0.762 A=0.238
SGDP_PRJ Global Study-wide 208 G=0.399 A=0.601
The Danish reference pan genome Danish Study-wide 40 G=0.75 A=0.25
Siberian Global Study-wide 34 G=0.32 A=0.68
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 3 NC_000003.12:g.126190572G>A
GRCh38.p14 chr 3 NC_000003.12:g.126190572G>C
GRCh37.p13 chr 3 NC_000003.11:g.125909415G>A
GRCh37.p13 chr 3 NC_000003.11:g.125909415G>C
Gene: ALDH1L1, aldehyde dehydrogenase 1 family member L1 (minus strand)
Molecule type Change Amino acid[Codon] SO Term
ALDH1L1 transcript variant 1 NM_001270364.2:c. N/A Genic Upstream Transcript Variant
ALDH1L1 transcript variant 3 NM_001270365.2:c. N/A Genic Upstream Transcript Variant
ALDH1L1 transcript variant 2 NM_012190.4:c. N/A Genic Upstream Transcript Variant
ALDH1L1 transcript variant 4 NR_072979.2:n. N/A Genic Upstream Transcript Variant
ALDH1L1 transcript variant X3 XM_024453325.2:c.-24+7163…

XM_024453325.2:c.-24+7163C>T

 		N/A Intron Variant
ALDH1L1 transcript variant X1 XM_006713481.4:c. N/A Genic Upstream Transcript Variant
ALDH1L1 transcript variant X2 XM_011512355.2:c. N/A Genic Upstream Transcript Variant
ALDH1L1 transcript variant X4 XM_017005613.3:c. N/A Genic Upstream Transcript Variant
ALDH1L1 transcript variant X5 XM_017005614.3:c. N/A Genic Upstream Transcript Variant
Gene: ALDH1L1-AS2, ALDH1L1 antisense RNA 2 (plus strand)
Molecule type Change Amino acid[Codon] SO Term
ALDH1L1-AS2 transcript NR_046383.1:n. 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 G= A C
GRCh38.p14 chr 3 NC_000003.12:g.126190572= NC_000003.12:g.126190572G>A NC_000003.12:g.126190572G>C
GRCh37.p13 chr 3 NC_000003.11:g.125909415= NC_000003.11:g.125909415G>A NC_000003.11:g.125909415G>C
ALDH1L1 transcript variant X3 XM_024453325.2:c.-24+7163= XM_024453325.2:c.-24+7163C>T XM_024453325.2:c.-24+7163C>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#.

90 SubSNP, 21 Frequency submissions
No Submitter Submission ID Date (Build)
1 SSAHASNP ss21915950 Apr 05, 2004 (121)
2 ABI ss42047001 Mar 13, 2006 (126)
3 PERLEGEN ss68874566 May 16, 2007 (127)
4 AFFY ss76446088 Dec 06, 2007 (129)
5 HGSV ss77548084 Dec 06, 2007 (129)
6 KRIBB_YJKIM ss105070843 Feb 05, 2009 (130)
7 ENSEMBL ss135518320 Dec 01, 2009 (131)
8 ILLUMINA ss160315373 Dec 01, 2009 (131)
9 BCM-HGSC-SUB ss206197894 Jul 04, 2010 (132)
10 1000GENOMES ss220408627 Jul 14, 2010 (132)
11 1000GENOMES ss232019055 Jul 14, 2010 (132)
12 1000GENOMES ss239393014 Jul 15, 2010 (132)
13 GMI ss277337232 May 04, 2012 (137)
14 PJP ss292907063 May 09, 2011 (134)
15 ILLUMINA ss479865289 May 04, 2012 (137)
16 ILLUMINA ss479873015 May 04, 2012 (137)
17 ILLUMINA ss480478080 Sep 08, 2015 (146)
18 ILLUMINA ss484731181 May 04, 2012 (137)
19 ILLUMINA ss536830251 Sep 08, 2015 (146)
20 SSMP ss650640877 Apr 25, 2013 (138)
21 ILLUMINA ss778420495 Sep 08, 2015 (146)
22 ILLUMINA ss782812274 Sep 08, 2015 (146)
23 ILLUMINA ss783777488 Sep 08, 2015 (146)
24 ILLUMINA ss832065488 Sep 08, 2015 (146)
25 ILLUMINA ss833875851 Sep 08, 2015 (146)
26 EVA-GONL ss979126201 Aug 21, 2014 (142)
27 JMKIDD_LAB ss1070806825 Aug 21, 2014 (142)
28 1000GENOMES ss1306017622 Aug 21, 2014 (142)
29 HAMMER_LAB ss1397351195 Sep 08, 2015 (146)
30 DDI ss1429577199 Apr 01, 2015 (144)
31 EVA_GENOME_DK ss1580168893 Apr 01, 2015 (144)
32 EVA_DECODE ss1588608778 Apr 01, 2015 (144)
33 EVA_UK10K_ALSPAC ss1608142407 Apr 01, 2015 (144)
34 EVA_UK10K_TWINSUK ss1651136440 Apr 01, 2015 (144)
35 EVA_SVP ss1712609901 Apr 01, 2015 (144)
36 ILLUMINA ss1752437636 Sep 08, 2015 (146)
37 WEILL_CORNELL_DGM ss1922351424 Feb 12, 2016 (147)
38 JJLAB ss2021744458 Sep 14, 2016 (149)
39 ILLUMINA ss2095137773 Dec 20, 2016 (150)
40 USC_VALOUEV ss2149837400 Dec 20, 2016 (150)
41 HUMAN_LONGEVITY ss2255549648 Dec 20, 2016 (150)
42 SYSTEMSBIOZJU ss2625374031 Nov 08, 2017 (151)
43 ILLUMINA ss2634007914 Nov 08, 2017 (151)
44 GRF ss2705244584 Nov 08, 2017 (151)
45 GNOMAD ss2798730877 Nov 08, 2017 (151)
46 AFFY ss2985892201 Nov 08, 2017 (151)
47 SWEGEN ss2993140776 Nov 08, 2017 (151)
48 BIOINF_KMB_FNS_UNIBA ss3024638901 Nov 08, 2017 (151)
49 CSHL ss3345250713 Nov 08, 2017 (151)
50 ILLUMINA ss3628768250 Oct 12, 2018 (152)
51 ILLUMINA ss3631950856 Oct 12, 2018 (152)
52 ILLUMINA ss3634025245 Oct 12, 2018 (152)
53 ILLUMINA ss3634915603 Oct 12, 2018 (152)
54 ILLUMINA ss3635708852 Oct 12, 2018 (152)
55 ILLUMINA ss3636611643 Oct 12, 2018 (152)
56 ILLUMINA ss3637461257 Oct 12, 2018 (152)
57 ILLUMINA ss3640622902 Oct 12, 2018 (152)
58 ILLUMINA ss3641151248 Oct 12, 2018 (152)
59 ILLUMINA ss3641447922 Oct 12, 2018 (152)
60 URBANLAB ss3647519548 Oct 12, 2018 (152)
61 ILLUMINA ss3652761750 Oct 12, 2018 (152)
62 EGCUT_WGS ss3661061977 Jul 13, 2019 (153)
63 EVA_DECODE ss3710221554 Jul 13, 2019 (153)
64 ACPOP ss3730321795 Jul 13, 2019 (153)
65 ILLUMINA ss3745215579 Jul 13, 2019 (153)
66 EVA ss3760649328 Jul 13, 2019 (153)
67 ILLUMINA ss3772710842 Jul 13, 2019 (153)
68 KHV_HUMAN_GENOMES ss3803784064 Jul 13, 2019 (153)
69 EVA ss3828058716 Apr 25, 2020 (154)
70 EVA ss3837460760 Apr 25, 2020 (154)
71 EVA ss3842891294 Apr 25, 2020 (154)
72 SGDP_PRJ ss3856896655 Apr 25, 2020 (154)
73 KRGDB ss3902903107 Apr 25, 2020 (154)
74 EVA ss4017104116 Apr 27, 2021 (155)
75 TOPMED ss4582448020 Apr 27, 2021 (155)
76 TOMMO_GENOMICS ss5161428926 Apr 27, 2021 (155)
77 1000G_HIGH_COVERAGE ss5255907142 Oct 12, 2022 (156)
78 EVA ss5314890971 Oct 12, 2022 (156)
79 EVA ss5343045838 Oct 12, 2022 (156)
80 HUGCELL_USP ss5455062335 Oct 12, 2022 (156)
81 EVA ss5507188136 Oct 12, 2022 (156)
82 1000G_HIGH_COVERAGE ss5535285394 Oct 12, 2022 (156)
83 SANFORD_IMAGENETICS ss5633122349 Oct 12, 2022 (156)
84 TOMMO_GENOMICS ss5694257550 Oct 12, 2022 (156)
85 EVA ss5799591425 Oct 12, 2022 (156)
86 YY_MCH ss5804215739 Oct 12, 2022 (156)
87 EVA ss5826435808 Oct 12, 2022 (156)
88 EVA ss5853823231 Oct 12, 2022 (156)
89 EVA ss5870863227 Oct 12, 2022 (156)
90 EVA ss5961468035 Oct 12, 2022 (156)
91 1000Genomes NC_000003.11 - 125909415 Oct 12, 2018 (152)
92 1000Genomes_30x NC_000003.12 - 126190572 Oct 12, 2022 (156)
93 The Avon Longitudinal Study of Parents and Children NC_000003.11 - 125909415 Oct 12, 2018 (152)
94 Chileans NC_000003.11 - 125909415 Apr 25, 2020 (154)
95 Genome-wide autozygosity in Daghestan NC_000003.10 - 127392105 Apr 25, 2020 (154)
96 Genetic variation in the Estonian population NC_000003.11 - 125909415 Oct 12, 2018 (152)
97 The Danish reference pan genome NC_000003.11 - 125909415 Apr 25, 2020 (154)
98 gnomAD - Genomes NC_000003.12 - 126190572 Apr 27, 2021 (155)
99 Genome of the Netherlands Release 5 NC_000003.11 - 125909415 Apr 25, 2020 (154)
100 HapMap NC_000003.12 - 126190572 Apr 25, 2020 (154)
101 KOREAN population from KRGDB NC_000003.11 - 125909415 Apr 25, 2020 (154)
102 Northern Sweden NC_000003.11 - 125909415 Jul 13, 2019 (153)
103 Qatari NC_000003.11 - 125909415 Apr 25, 2020 (154)
104 SGDP_PRJ NC_000003.11 - 125909415 Apr 25, 2020 (154)
105 Siberian NC_000003.11 - 125909415 Apr 25, 2020 (154)
106 8.3KJPN NC_000003.11 - 125909415 Apr 27, 2021 (155)
107 14KJPN NC_000003.12 - 126190572 Oct 12, 2022 (156)
108 TopMed NC_000003.12 - 126190572 Apr 27, 2021 (155)
109 UK 10K study - Twins NC_000003.11 - 125909415 Oct 12, 2018 (152)
110 A Vietnamese Genetic Variation Database NC_000003.11 - 125909415 Jul 13, 2019 (153)
111 ALFA NC_000003.12 - 126190572 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
ss77548084 NC_000003.9:127392112:G:A NC_000003.12:126190571:G:A (self)
327021, ss76446088, ss206197894, ss277337232, ss292907063, ss479865289, ss1397351195, ss1588608778, ss1712609901 NC_000003.10:127392104:G:A NC_000003.12:126190571:G:A (self)
17275675, 9623669, 295599, 6800225, 6333832, 4229113, 10080501, 3606660, 4393354, 8913635, 2353754, 19398233, 9623669, 2097960, ss220408627, ss232019055, ss239393014, ss479873015, ss480478080, ss484731181, ss536830251, ss650640877, ss778420495, ss782812274, ss783777488, ss832065488, ss833875851, ss979126201, ss1070806825, ss1306017622, ss1429577199, ss1580168893, ss1608142407, ss1651136440, ss1752437636, ss1922351424, ss2021744458, ss2095137773, ss2149837400, ss2625374031, ss2634007914, ss2705244584, ss2798730877, ss2985892201, ss2993140776, ss3345250713, ss3628768250, ss3631950856, ss3634025245, ss3634915603, ss3635708852, ss3636611643, ss3637461257, ss3640622902, ss3641151248, ss3641447922, ss3652761750, ss3661061977, ss3730321795, ss3745215579, ss3760649328, ss3772710842, ss3828058716, ss3837460760, ss3856896655, ss3902903107, ss4017104116, ss5161428926, ss5314890971, ss5343045838, ss5507188136, ss5633122349, ss5799591425, ss5826435808, ss5961468035 NC_000003.11:125909414:G:A NC_000003.12:126190571:G:A (self)
22811329, 122806979, 2452981, 28094654, 419825575, 10203207255, ss2255549648, ss3024638901, ss3647519548, ss3710221554, ss3803784064, ss3842891294, ss4582448020, ss5255907142, ss5455062335, ss5535285394, ss5694257550, ss5804215739, ss5853823231, ss5870863227 NC_000003.12:126190571:G:A NC_000003.12:126190571:G:A (self)
ss21915950 NT_005612.14:32404568:G:A NC_000003.12:126190571:G:A (self)
ss42047001, ss68874566, ss105070843, ss135518320, ss160315373 NT_005612.16:32404560:G:A NC_000003.12:126190571:G:A (self)
10203207255 NC_000003.12:126190571:G:C NC_000003.12:126190571: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 rs13070856

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