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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.

rs10519915

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr5:126594115 (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
T>C
Variation Type
SNV Single Nucleotide Variation
Frequency
C=0.055846 (14782/264690, TOPMED)
C=0.057991 (8131/140212, GnomAD)
C=0.06873 (2728/39694, ALFA) (+ 17 more)
C=0.00630 (178/28258, 14KJPN)
C=0.00650 (109/16760, 8.3KJPN)
C=0.0443 (284/6404, 1000G_30x)
C=0.0463 (232/5008, 1000G)
C=0.1013 (454/4480, Estonian)
C=0.0727 (280/3854, ALSPAC)
C=0.0809 (300/3708, TWINSUK)
C=0.0099 (29/2922, KOREAN)
C=0.065 (65/998, GoNL)
C=0.087 (52/600, NorthernSweden)
C=0.073 (39/534, MGP)
C=0.037 (12/328, HapMap)
C=0.060 (13/216, Qatari)
T=0.44 (30/68, SGDP_PRJ)
C=0.05 (2/40, GENOME_DK)
T=0.5 (4/8, Siberian)
C=0.5 (4/8, Siberian)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
ALDH7A1 : 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 39766 T=0.93120 C=0.06880
European Sub 30702 T=0.92222 C=0.07778
African Sub 5800 T=0.9702 C=0.0298
African Others Sub 206 T=0.966 C=0.034
African American Sub 5594 T=0.9703 C=0.0297
Asian Sub 128 T=0.992 C=0.008
East Asian Sub 100 T=1.00 C=0.00
Other Asian Sub 28 T=0.96 C=0.04
Latin American 1 Sub 168 T=0.905 C=0.095
Latin American 2 Sub 700 T=0.960 C=0.040
South Asian Sub 114 T=0.860 C=0.140
Other Sub 2154 T=0.9471 C=0.0529


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 T=0.944154 C=0.055846
gnomAD - Genomes Global Study-wide 140212 T=0.942009 C=0.057991
gnomAD - Genomes European Sub 75930 T=0.92423 C=0.07577
gnomAD - Genomes African Sub 42030 T=0.96936 C=0.03064
gnomAD - Genomes American Sub 13642 T=0.93806 C=0.06194
gnomAD - Genomes Ashkenazi Jewish Sub 3324 T=0.9639 C=0.0361
gnomAD - Genomes East Asian Sub 3132 T=0.9949 C=0.0051
gnomAD - Genomes Other Sub 2154 T=0.9494 C=0.0506
Allele Frequency Aggregator Total Global 39694 T=0.93127 C=0.06873
Allele Frequency Aggregator European Sub 30644 T=0.92227 C=0.07773
Allele Frequency Aggregator African Sub 5800 T=0.9702 C=0.0298
Allele Frequency Aggregator Other Sub 2140 T=0.9477 C=0.0523
Allele Frequency Aggregator Latin American 2 Sub 700 T=0.960 C=0.040
Allele Frequency Aggregator Latin American 1 Sub 168 T=0.905 C=0.095
Allele Frequency Aggregator Asian Sub 128 T=0.992 C=0.008
Allele Frequency Aggregator South Asian Sub 114 T=0.860 C=0.140
14KJPN JAPANESE Study-wide 28258 T=0.99370 C=0.00630
8.3KJPN JAPANESE Study-wide 16760 T=0.99350 C=0.00650
1000Genomes_30x Global Study-wide 6404 T=0.9557 C=0.0443
1000Genomes_30x African Sub 1786 T=0.9804 C=0.0196
1000Genomes_30x Europe Sub 1266 T=0.9273 C=0.0727
1000Genomes_30x South Asian Sub 1202 T=0.9035 C=0.0965
1000Genomes_30x East Asian Sub 1170 T=0.9983 C=0.0017
1000Genomes_30x American Sub 980 T=0.960 C=0.040
1000Genomes Global Study-wide 5008 T=0.9537 C=0.0463
1000Genomes African Sub 1322 T=0.9788 C=0.0212
1000Genomes East Asian Sub 1008 T=0.9980 C=0.0020
1000Genomes Europe Sub 1006 T=0.9254 C=0.0746
1000Genomes South Asian Sub 978 T=0.899 C=0.101
1000Genomes American Sub 694 T=0.960 C=0.040
Genetic variation in the Estonian population Estonian Study-wide 4480 T=0.8987 C=0.1013
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 T=0.9273 C=0.0727
UK 10K study - Twins TWIN COHORT Study-wide 3708 T=0.9191 C=0.0809
KOREAN population from KRGDB KOREAN Study-wide 2922 T=0.9901 C=0.0099
Genome of the Netherlands Release 5 Genome of the Netherlands Study-wide 998 T=0.935 C=0.065
Northern Sweden ACPOP Study-wide 600 T=0.913 C=0.087
Medical Genome Project healthy controls from Spanish population Spanish controls Study-wide 534 T=0.927 C=0.073
HapMap Global Study-wide 328 T=0.963 C=0.037
HapMap African Sub 120 T=0.958 C=0.042
HapMap American Sub 120 T=0.950 C=0.050
HapMap Asian Sub 88 T=0.99 C=0.01
Qatari Global Study-wide 216 T=0.940 C=0.060
SGDP_PRJ Global Study-wide 68 T=0.44 C=0.56
The Danish reference pan genome Danish Study-wide 40 T=0.95 C=0.05
Siberian Global Study-wide 8 T=0.5 C=0.5
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.126594115T>C
GRCh37.p13 chr 5 NC_000005.9:g.125929807T>C
ALDH7A1 RefSeqGene NG_008600.3:g.6276A>G
Gene: ALDH7A1, aldehyde dehydrogenase 7 family member A1 (minus strand)
Molecule type Change Amino acid[Codon] SO Term
ALDH7A1 transcript variant 1 NM_001182.5:c.193-711A>G N/A Intron Variant
ALDH7A1 transcript variant 1 NM_001201377.2:c.109-711A…

NM_001201377.2:c.109-711A>G

N/A Intron Variant
ALDH7A1 transcript variant 2 NM_001202404.2:c.193-711A…

NM_001202404.2:c.193-711A>G

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 T= C
GRCh38.p14 chr 5 NC_000005.10:g.126594115= NC_000005.10:g.126594115T>C
GRCh37.p13 chr 5 NC_000005.9:g.125929807= NC_000005.9:g.125929807T>C
ALDH7A1 RefSeqGene NG_008600.3:g.6276= NG_008600.3:g.6276A>G
ALDH7A1 transcript variant 1 NM_001182.4:c.193-711= NM_001182.4:c.193-711A>G
ALDH7A1 transcript variant 1 NM_001182.5:c.193-711= NM_001182.5:c.193-711A>G
ALDH7A1 transcript variant 1 NM_001201377.1:c.109-711= NM_001201377.1:c.109-711A>G
ALDH7A1 transcript variant 1 NM_001201377.2:c.109-711= NM_001201377.2:c.109-711A>G
ALDH7A1 transcript variant 2 NM_001202404.1:c.274-711= NM_001202404.1:c.274-711A>G
ALDH7A1 transcript variant 2 NM_001202404.2:c.193-711= NM_001202404.2:c.193-711A>G
ALDH7A1 transcript variant X1 XM_005271993.1:c.274-711= XM_005271993.1:c.274-711A>G
ALDH7A1 transcript variant X2 XM_005271994.1:c.274-711= XM_005271994.1:c.274-711A>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#.

69 SubSNP, 19 Frequency submissions
No Submitter Submission ID Date (Build)
1 PERLEGEN ss14922458 Dec 05, 2003 (119)
2 PERLEGEN ss24365678 Sep 20, 2004 (123)
3 AFFY ss66020367 Nov 29, 2006 (127)
4 BCMHGSC_JDW ss93244302 Mar 24, 2008 (129)
5 ENSEMBL ss143429946 Dec 01, 2009 (131)
6 COMPLETE_GENOMICS ss162646855 Jul 04, 2010 (132)
7 COMPLETE_GENOMICS ss167056753 Jul 04, 2010 (132)
8 1000GENOMES ss221949791 Jul 14, 2010 (132)
9 1000GENOMES ss233139181 Jul 14, 2010 (132)
10 ILLUMINA ss483569624 May 04, 2012 (137)
11 ILLUMINA ss484929526 May 04, 2012 (137)
12 ILLUMINA ss535775815 Sep 08, 2015 (146)
13 TISHKOFF ss558695695 Apr 25, 2013 (138)
14 SSMP ss652592155 Apr 25, 2013 (138)
15 ILLUMINA ss780326927 Sep 08, 2015 (146)
16 ILLUMINA ss782228275 Sep 08, 2015 (146)
17 ILLUMINA ss835814181 Sep 08, 2015 (146)
18 EVA-GONL ss982092276 Aug 21, 2014 (142)
19 JMKIDD_LAB ss1073020453 Aug 21, 2014 (142)
20 1000GENOMES ss1317088815 Aug 21, 2014 (142)
21 EVA_GENOME_DK ss1581339864 Apr 01, 2015 (144)
22 EVA_DECODE ss1591617615 Apr 01, 2015 (144)
23 EVA_UK10K_ALSPAC ss1613943690 Apr 01, 2015 (144)
24 EVA_UK10K_TWINSUK ss1656937723 Apr 01, 2015 (144)
25 EVA_MGP ss1711096214 Apr 01, 2015 (144)
26 WEILL_CORNELL_DGM ss1925348790 Feb 12, 2016 (147)
27 JJLAB ss2023280783 Sep 14, 2016 (149)
28 USC_VALOUEV ss2151436696 Dec 20, 2016 (150)
29 HUMAN_LONGEVITY ss2277879931 Dec 20, 2016 (150)
30 ILLUMINA ss2634336425 Nov 08, 2017 (151)
31 GRF ss2706998179 Nov 08, 2017 (151)
32 GNOMAD ss2830395366 Nov 08, 2017 (151)
33 AFFY ss2985333341 Nov 08, 2017 (151)
34 AFFY ss2985966763 Nov 08, 2017 (151)
35 SWEGEN ss2997742387 Nov 08, 2017 (151)
36 BIOINF_KMB_FNS_UNIBA ss3025423917 Nov 08, 2017 (151)
37 CSHL ss3346615145 Nov 08, 2017 (151)
38 ILLUMINA ss3629334626 Oct 12, 2018 (152)
39 ILLUMINA ss3632260694 Oct 12, 2018 (152)
40 ILLUMINA ss3642443635 Oct 12, 2018 (152)
41 OMUKHERJEE_ADBS ss3646323969 Oct 12, 2018 (152)
42 URBANLAB ss3648164347 Oct 12, 2018 (152)
43 ILLUMINA ss3654105716 Oct 12, 2018 (152)
44 EGCUT_WGS ss3665652851 Jul 13, 2019 (153)
45 EVA_DECODE ss3715640899 Jul 13, 2019 (153)
46 ACPOP ss3732791382 Jul 13, 2019 (153)
47 EVA ss3764024210 Jul 13, 2019 (153)
48 KHV_HUMAN_GENOMES ss3807198705 Jul 13, 2019 (153)
49 EVA ss3825678884 Apr 26, 2020 (154)
50 EVA ss3829491177 Apr 26, 2020 (154)
51 SGDP_PRJ ss3862912617 Apr 26, 2020 (154)
52 KRGDB ss3909541701 Apr 26, 2020 (154)
53 FSA-LAB ss3984314413 Apr 26, 2021 (155)
54 EVA ss3986317074 Apr 26, 2021 (155)
55 TOPMED ss4677560835 Apr 26, 2021 (155)
56 TOMMO_GENOMICS ss5173992326 Apr 26, 2021 (155)
57 1000G_HIGH_COVERAGE ss5265729925 Oct 13, 2022 (156)
58 EVA ss5315084337 Oct 13, 2022 (156)
59 EVA ss5360757713 Oct 13, 2022 (156)
60 HUGCELL_USP ss5463709943 Oct 13, 2022 (156)
61 1000G_HIGH_COVERAGE ss5550318837 Oct 13, 2022 (156)
62 SANFORD_IMAGENETICS ss5638820714 Oct 13, 2022 (156)
63 TOMMO_GENOMICS ss5711024883 Oct 13, 2022 (156)
64 YY_MCH ss5806740753 Oct 13, 2022 (156)
65 EVA ss5835600401 Oct 13, 2022 (156)
66 EVA ss5848633476 Oct 13, 2022 (156)
67 EVA ss5855006252 Oct 13, 2022 (156)
68 EVA ss5896191153 Oct 13, 2022 (156)
69 EVA ss5967282989 Oct 13, 2022 (156)
70 1000Genomes NC_000005.9 - 125929807 Oct 12, 2018 (152)
71 1000Genomes_30x NC_000005.10 - 126594115 Oct 13, 2022 (156)
72 The Avon Longitudinal Study of Parents and Children NC_000005.9 - 125929807 Oct 12, 2018 (152)
73 Genetic variation in the Estonian population NC_000005.9 - 125929807 Oct 12, 2018 (152)
74 The Danish reference pan genome NC_000005.9 - 125929807 Apr 26, 2020 (154)
75 gnomAD - Genomes NC_000005.10 - 126594115 Apr 26, 2021 (155)
76 Genome of the Netherlands Release 5 NC_000005.9 - 125929807 Apr 26, 2020 (154)
77 HapMap NC_000005.10 - 126594115 Apr 26, 2020 (154)
78 KOREAN population from KRGDB NC_000005.9 - 125929807 Apr 26, 2020 (154)
79 Medical Genome Project healthy controls from Spanish population NC_000005.9 - 125929807 Apr 26, 2020 (154)
80 Northern Sweden NC_000005.9 - 125929807 Jul 13, 2019 (153)
81 Qatari NC_000005.9 - 125929807 Apr 26, 2020 (154)
82 SGDP_PRJ NC_000005.9 - 125929807 Apr 26, 2020 (154)
83 Siberian NC_000005.9 - 125929807 Apr 26, 2020 (154)
84 8.3KJPN NC_000005.9 - 125929807 Apr 26, 2021 (155)
85 14KJPN NC_000005.10 - 126594115 Oct 13, 2022 (156)
86 TopMed NC_000005.10 - 126594115 Apr 26, 2021 (155)
87 UK 10K study - Twins NC_000005.9 - 125929807 Oct 12, 2018 (152)
88 ALFA NC_000005.10 - 126594115 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)
rs17597946 Oct 08, 2004 (123)
Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
ss93244302, ss162646855, ss167056753, ss484929526, ss1591617615 NC_000005.8:125957705:T:C NC_000005.10:126594114:T:C (self)
28762761, 15996957, 11391099, 7504803, 7112197, 16719095, 211974, 6076247, 7390720, 14929597, 3953050, 31961633, 15996957, ss221949791, ss233139181, ss483569624, ss535775815, ss558695695, ss652592155, ss780326927, ss782228275, ss835814181, ss982092276, ss1073020453, ss1317088815, ss1581339864, ss1613943690, ss1656937723, ss1711096214, ss1925348790, ss2023280783, ss2151436696, ss2634336425, ss2706998179, ss2830395366, ss2985333341, ss2985966763, ss2997742387, ss3346615145, ss3629334626, ss3632260694, ss3642443635, ss3646323969, ss3654105716, ss3665652851, ss3732791382, ss3764024210, ss3825678884, ss3829491177, ss3862912617, ss3909541701, ss3984314413, ss3986317074, ss5173992326, ss5315084337, ss5360757713, ss5638820714, ss5835600401, ss5848633476, ss5967282989 NC_000005.9:125929806:T:C NC_000005.10:126594114:T:C (self)
37844772, 203415151, 2962982, 44861987, 514938392, 6715552389, ss2277879931, ss3025423917, ss3648164347, ss3715640899, ss3807198705, ss4677560835, ss5265729925, ss5463709943, ss5550318837, ss5711024883, ss5806740753, ss5855006252, ss5896191153 NC_000005.10:126594114:T:C NC_000005.10:126594114:T:C (self)
ss14922458, ss24365678, ss66020367, ss143429946 NT_034772.6:34243678:T:C NC_000005.10:126594114:T: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 rs10519915

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