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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.

rs10430124

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr1:45755945 (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>T
Variation Type
SNV Single Nucleotide Variation
Frequency
A=0.284593 (75329/264690, TOPMED)
A=0.36252 (10244/28258, 14KJPN)
A=0.20773 (3887/18712, ALFA) (+ 17 more)
A=0.36301 (6084/16760, 8.3KJPN)
A=0.3200 (2049/6404, 1000G_30x)
A=0.3191 (1598/5008, 1000G)
A=0.2848 (1276/4480, Estonian)
A=0.3080 (1187/3854, ALSPAC)
A=0.3029 (1123/3708, TWINSUK)
A=0.3126 (916/2930, KOREAN)
A=0.3208 (607/1892, HapMap)
A=0.3062 (561/1832, Korea1K)
A=0.287 (286/998, GoNL)
A=0.374 (234/626, Chileans)
A=0.318 (191/600, NorthernSweden)
G=0.341 (107/314, SGDP_PRJ)
A=0.435 (94/216, Qatari)
A=0.358 (76/212, Vietnamese)
A=0.33 (13/40, GENOME_DK)
G=0.39 (11/28, Siberian)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
LOC105378693 : 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 18712 G=0.79227 A=0.20773, T=0.00000
European Sub 12132 G=0.79097 A=0.20903, T=0.00000
African Sub 2634 G=0.8785 A=0.1215, T=0.0000
African Others Sub 98 G=0.90 A=0.10, T=0.00
African American Sub 2536 G=0.8778 A=0.1222, T=0.0000
Asian Sub 98 G=0.67 A=0.33, T=0.00
East Asian Sub 58 G=0.90 A=0.10, T=0.00
Other Asian Sub 40 G=0.35 A=0.65, T=0.00
Latin American 1 Sub 210 G=0.757 A=0.243, T=0.000
Latin American 2 Sub 2466 G=0.7186 A=0.2814, T=0.0000
South Asian Sub 50 G=0.92 A=0.08, T=0.00
Other Sub 1122 G=0.7772 A=0.2228, 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 G=0.715407 A=0.284593
14KJPN JAPANESE Study-wide 28258 G=0.63748 A=0.36252
Allele Frequency Aggregator Total Global 18712 G=0.79227 A=0.20773, T=0.00000
Allele Frequency Aggregator European Sub 12132 G=0.79097 A=0.20903, T=0.00000
Allele Frequency Aggregator African Sub 2634 G=0.8785 A=0.1215, T=0.0000
Allele Frequency Aggregator Latin American 2 Sub 2466 G=0.7186 A=0.2814, T=0.0000
Allele Frequency Aggregator Other Sub 1122 G=0.7772 A=0.2228, T=0.0000
Allele Frequency Aggregator Latin American 1 Sub 210 G=0.757 A=0.243, T=0.000
Allele Frequency Aggregator Asian Sub 98 G=0.67 A=0.33, T=0.00
Allele Frequency Aggregator South Asian Sub 50 G=0.92 A=0.08, T=0.00
8.3KJPN JAPANESE Study-wide 16760 G=0.63699 A=0.36301
1000Genomes_30x Global Study-wide 6404 G=0.6800 A=0.3200
1000Genomes_30x African Sub 1786 G=0.7503 A=0.2497
1000Genomes_30x Europe Sub 1266 G=0.7125 A=0.2875
1000Genomes_30x South Asian Sub 1202 G=0.5940 A=0.4060
1000Genomes_30x East Asian Sub 1170 G=0.6470 A=0.3530
1000Genomes_30x American Sub 980 G=0.655 A=0.345
1000Genomes Global Study-wide 5008 G=0.6809 A=0.3191
1000Genomes African Sub 1322 G=0.7496 A=0.2504
1000Genomes East Asian Sub 1008 G=0.6607 A=0.3393
1000Genomes Europe Sub 1006 G=0.7147 A=0.2853
1000Genomes South Asian Sub 978 G=0.593 A=0.407
1000Genomes American Sub 694 G=0.654 A=0.346
Genetic variation in the Estonian population Estonian Study-wide 4480 G=0.7152 A=0.2848
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 G=0.6920 A=0.3080
UK 10K study - Twins TWIN COHORT Study-wide 3708 G=0.6971 A=0.3029
KOREAN population from KRGDB KOREAN Study-wide 2930 G=0.6874 A=0.3126
HapMap Global Study-wide 1892 G=0.6792 A=0.3208
HapMap American Sub 770 G=0.660 A=0.340
HapMap African Sub 692 G=0.702 A=0.298
HapMap Asian Sub 254 G=0.646 A=0.354
HapMap Europe Sub 176 G=0.722 A=0.278
Korean Genome Project KOREAN Study-wide 1832 G=0.6938 A=0.3062
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=0.626 A=0.374
Northern Sweden ACPOP Study-wide 600 G=0.682 A=0.318
SGDP_PRJ Global Study-wide 314 G=0.341 A=0.659
Qatari Global Study-wide 216 G=0.565 A=0.435
A Vietnamese Genetic Variation Database Global Study-wide 212 G=0.642 A=0.358
The Danish reference pan genome Danish Study-wide 40 G=0.68 A=0.33
Siberian Global Study-wide 28 G=0.39 A=0.61
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.45755945G>A
GRCh38.p14 chr 1 NC_000001.11:g.45755945G>T
GRCh37.p13 chr 1 NC_000001.10:g.46221617G>A
GRCh37.p13 chr 1 NC_000001.10:g.46221617G>T
Gene: LOC105378693, uncharacterized LOC105378693 (plus strand)
Molecule type Change Amino acid[Codon] SO Term
LOC105378693 transcript variant X1 XR_947289.2:n. N/A Intron Variant
LOC105378693 transcript variant X2 XR_947290.2: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 T
GRCh38.p14 chr 1 NC_000001.11:g.45755945= NC_000001.11:g.45755945G>A NC_000001.11:g.45755945G>T
GRCh37.p13 chr 1 NC_000001.10:g.46221617= NC_000001.10:g.46221617G>A NC_000001.10:g.46221617G>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#.

64 SubSNP, 22 Frequency submissions
No Submitter Submission ID Date (Build)
1 SC_SNP ss14736359 Dec 05, 2003 (119)
2 SC_SNP ss19825519 Feb 28, 2004 (126)
3 AFFY ss76593431 Dec 07, 2007 (129)
4 BCMHGSC_JDW ss87400346 Mar 23, 2008 (129)
5 BGI ss102738174 Dec 01, 2009 (131)
6 KRIBB_YJKIM ss105007280 Feb 05, 2009 (130)
7 1000GENOMES ss108167176 Jan 23, 2009 (130)
8 1000GENOMES ss110377556 Jan 24, 2009 (130)
9 ILLUMINA-UK ss118660252 Feb 14, 2009 (130)
10 ENSEMBL ss137914413 Dec 01, 2009 (131)
11 COMPLETE_GENOMICS ss163338187 Jul 04, 2010 (132)
12 COMPLETE_GENOMICS ss164206146 Jul 04, 2010 (132)
13 1000GENOMES ss218356284 Jul 14, 2010 (132)
14 1000GENOMES ss230514234 Jul 14, 2010 (132)
15 1000GENOMES ss238212779 Jul 15, 2010 (132)
16 GMI ss275806246 May 04, 2012 (137)
17 GMI ss284041870 Apr 25, 2013 (138)
18 TISHKOFF ss554058231 Apr 25, 2013 (138)
19 SSMP ss647851707 Apr 25, 2013 (138)
20 EVA-GONL ss975100335 Aug 21, 2014 (142)
21 JMKIDD_LAB ss1067842616 Aug 21, 2014 (142)
22 1000GENOMES ss1290648533 Aug 21, 2014 (142)
23 DDI ss1425791110 Apr 01, 2015 (144)
24 EVA_GENOME_DK ss1574026039 Apr 01, 2015 (144)
25 EVA_DECODE ss1584464285 Apr 01, 2015 (144)
26 EVA_UK10K_ALSPAC ss1600047714 Apr 01, 2015 (144)
27 EVA_UK10K_TWINSUK ss1643041747 Apr 01, 2015 (144)
28 EVA_SVP ss1712328719 Apr 01, 2015 (144)
29 HAMMER_LAB ss1794274727 Sep 08, 2015 (146)
30 WEILL_CORNELL_DGM ss1918308556 Feb 12, 2016 (147)
31 GENOMED ss1966734465 Jul 19, 2016 (147)
32 JJLAB ss2019669730 Sep 14, 2016 (149)
33 USC_VALOUEV ss2147681873 Dec 20, 2016 (150)
34 HUMAN_LONGEVITY ss2161997507 Dec 20, 2016 (150)
35 GRF ss2697591941 Nov 08, 2017 (151)
36 GNOMAD ss2754444732 Nov 08, 2017 (151)
37 SWEGEN ss2986718094 Nov 08, 2017 (151)
38 BIOINF_KMB_FNS_UNIBA ss3023597427 Nov 08, 2017 (151)
39 CSHL ss3343429980 Nov 08, 2017 (151)
40 EGCUT_WGS ss3654783069 Jul 12, 2019 (153)
41 EVA_DECODE ss3686654689 Jul 12, 2019 (153)
42 ACPOP ss3726996701 Jul 12, 2019 (153)
43 EVA ss3746128550 Jul 12, 2019 (153)
44 KHV_HUMAN_GENOMES ss3799140956 Jul 12, 2019 (153)
45 EVA ss3826144381 Apr 25, 2020 (154)
46 EVA ss3836459475 Apr 25, 2020 (154)
47 EVA ss3841865206 Apr 25, 2020 (154)
48 SGDP_PRJ ss3848724103 Apr 25, 2020 (154)
49 KRGDB ss3893708211 Apr 25, 2020 (154)
50 KOGIC ss3944382532 Apr 25, 2020 (154)
51 TOPMED ss4447527871 Apr 25, 2021 (155)
52 TOMMO_GENOMICS ss5143664454 Apr 25, 2021 (155)
53 1000G_HIGH_COVERAGE ss5242057934 Oct 17, 2022 (156)
54 EVA ss5318335047 Oct 17, 2022 (156)
55 HUGCELL_USP ss5443144715 Oct 17, 2022 (156)
56 EVA ss5505830911 Oct 17, 2022 (156)
57 1000G_HIGH_COVERAGE ss5514224291 Oct 17, 2022 (156)
58 SANFORD_IMAGENETICS ss5625410809 Oct 17, 2022 (156)
59 TOMMO_GENOMICS ss5668348900 Oct 17, 2022 (156)
60 YY_MCH ss5800543158 Oct 17, 2022 (156)
61 EVA ss5831878661 Oct 17, 2022 (156)
62 EVA ss5848882758 Oct 17, 2022 (156)
63 EVA ss5908015325 Oct 17, 2022 (156)
64 EVA ss5937237276 Oct 17, 2022 (156)
65 1000Genomes NC_000001.10 - 46221617 Oct 11, 2018 (152)
66 1000Genomes_30x NC_000001.11 - 45755945 Oct 17, 2022 (156)
67 The Avon Longitudinal Study of Parents and Children NC_000001.10 - 46221617 Oct 11, 2018 (152)
68 Chileans NC_000001.10 - 46221617 Apr 25, 2020 (154)
69 Genetic variation in the Estonian population NC_000001.10 - 46221617 Oct 11, 2018 (152)
70 The Danish reference pan genome NC_000001.10 - 46221617 Apr 25, 2020 (154)
71 gnomAD - Genomes

Submission ignored due to conflicting rows:
Row 9586776 (NC_000001.11:45755944:G:A 39139/139886)
Row 9586777 (NC_000001.11:45755944:G:T 1/139948)

- Apr 25, 2021 (155)
72 gnomAD - Genomes

Submission ignored due to conflicting rows:
Row 9586776 (NC_000001.11:45755944:G:A 39139/139886)
Row 9586777 (NC_000001.11:45755944:G:T 1/139948)

- Apr 25, 2021 (155)
73 Genome of the Netherlands Release 5 NC_000001.10 - 46221617 Apr 25, 2020 (154)
74 HapMap NC_000001.11 - 45755945 Apr 25, 2020 (154)
75 KOREAN population from KRGDB NC_000001.10 - 46221617 Apr 25, 2020 (154)
76 Korean Genome Project NC_000001.11 - 45755945 Apr 25, 2020 (154)
77 Northern Sweden NC_000001.10 - 46221617 Jul 12, 2019 (153)
78 Qatari NC_000001.10 - 46221617 Apr 25, 2020 (154)
79 SGDP_PRJ NC_000001.10 - 46221617 Apr 25, 2020 (154)
80 Siberian NC_000001.10 - 46221617 Apr 25, 2020 (154)
81 8.3KJPN NC_000001.10 - 46221617 Apr 25, 2021 (155)
82 14KJPN NC_000001.11 - 45755945 Oct 17, 2022 (156)
83 TopMed NC_000001.11 - 45755945 Apr 25, 2021 (155)
84 UK 10K study - Twins NC_000001.10 - 46221617 Oct 11, 2018 (152)
85 A Vietnamese Genetic Variation Database NC_000001.10 - 46221617 Jul 12, 2019 (153)
86 ALFA NC_000001.11 - 45755945 Apr 25, 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)
rs12560266 Mar 11, 2006 (126)
Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
ss87400346, ss108167176, ss110377556, ss118660252, ss163338187, ss164206146, ss275806246, ss284041870, ss1584464285, ss1712328719 NC_000001.9:45994203:G:A NC_000001.11:45755944:G:A (self)
1358408, 738043, 6997, 521317, 1480606, 313766, 885605, 281566, 350486, 741083, 198227, 1633761, 738043, 151276, ss218356284, ss230514234, ss238212779, ss554058231, ss647851707, ss975100335, ss1067842616, ss1290648533, ss1425791110, ss1574026039, ss1600047714, ss1643041747, ss1794274727, ss1918308556, ss1966734465, ss2019669730, ss2147681873, ss2697591941, ss2754444732, ss2986718094, ss3343429980, ss3654783069, ss3726996701, ss3746128550, ss3826144381, ss3836459475, ss3848724103, ss3893708211, ss5143664454, ss5318335047, ss5505830911, ss5625410809, ss5831878661, ss5937237276 NC_000001.10:46221616:G:A NC_000001.11:45755944:G:A (self)
1750226, 57437, 760533, 2186004, 11134206, 9124712032, ss2161997507, ss3023597427, ss3686654689, ss3799140956, ss3841865206, ss3944382532, ss4447527871, ss5242057934, ss5443144715, ss5514224291, ss5668348900, ss5800543158, ss5848882758, ss5908015325 NC_000001.11:45755944:G:A NC_000001.11:45755944:G:A (self)
ss14736359 NT_032977.6:7784686:G:A NC_000001.11:45755944:G:A (self)
ss19825519, ss76593431, ss102738174, ss105007280, ss137914413 NT_032977.9:16193534:G:A NC_000001.11:45755944:G:A (self)
9124712032 NC_000001.11:45755944:G:T NC_000001.11:45755944:G: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 rs10430124

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