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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.

rs12116430

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr1:41996176 (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 / T>G
Variation Type
SNV Single Nucleotide Variation
Frequency
C=0.197102 (52171/264690, TOPMED)
C=0.185998 (25981/139684, GnomAD)
C=0.33297 (9409/28258, 14KJPN) (+ 15 more)
C=0.17345 (3213/18524, ALFA)
C=0.33156 (5557/16760, 8.3KJPN)
C=0.2408 (1542/6404, 1000G_30x)
C=0.2460 (1232/5008, 1000G)
C=0.1711 (766/4478, Estonian)
C=0.1720 (663/3854, ALSPAC)
C=0.1642 (609/3708, TWINSUK)
C=0.2720 (797/2930, KOREAN)
C=0.157 (157/998, GoNL)
C=0.185 (111/600, NorthernSweden)
C=0.259 (56/216, Qatari)
C=0.250 (53/212, Vietnamese)
T=0.441 (90/204, SGDP_PRJ)
C=0.28 (11/40, GENOME_DK)
T=0.41 (9/22, Siberian)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
HIVEP3 : Intron Variant
LOC124904160 : 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 18524 T=0.82655 C=0.17345, G=0.00000
European Sub 14084 T=0.83293 C=0.16707, G=0.00000
African Sub 2786 T=0.8453 C=0.1547, G=0.0000
African Others Sub 102 T=0.873 C=0.127, G=0.000
African American Sub 2684 T=0.8443 C=0.1557, G=0.0000
Asian Sub 112 T=0.795 C=0.205, G=0.000
East Asian Sub 86 T=0.78 C=0.22, G=0.00
Other Asian Sub 26 T=0.85 C=0.15, G=0.00
Latin American 1 Sub 146 T=0.733 C=0.267, G=0.000
Latin American 2 Sub 610 T=0.679 C=0.321, G=0.000
South Asian Sub 98 T=0.72 C=0.28, G=0.00
Other Sub 688 T=0.791 C=0.209, G=0.000


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=0.802898 C=0.197102
gnomAD - Genomes Global Study-wide 139684 T=0.814002 C=0.185998
gnomAD - Genomes European Sub 75718 T=0.82813 C=0.17187
gnomAD - Genomes African Sub 41820 T=0.82281 C=0.17719
gnomAD - Genomes American Sub 13574 T=0.72293 C=0.27707
gnomAD - Genomes Ashkenazi Jewish Sub 3318 T=0.8077 C=0.1923
gnomAD - Genomes East Asian Sub 3118 T=0.7733 C=0.2267
gnomAD - Genomes Other Sub 2136 T=0.7889 C=0.2111
14KJPN JAPANESE Study-wide 28258 T=0.66703 C=0.33297
Allele Frequency Aggregator Total Global 18524 T=0.82655 C=0.17345, G=0.00000
Allele Frequency Aggregator European Sub 14084 T=0.83293 C=0.16707, G=0.00000
Allele Frequency Aggregator African Sub 2786 T=0.8453 C=0.1547, G=0.0000
Allele Frequency Aggregator Other Sub 688 T=0.791 C=0.209, G=0.000
Allele Frequency Aggregator Latin American 2 Sub 610 T=0.679 C=0.321, G=0.000
Allele Frequency Aggregator Latin American 1 Sub 146 T=0.733 C=0.267, G=0.000
Allele Frequency Aggregator Asian Sub 112 T=0.795 C=0.205, G=0.000
Allele Frequency Aggregator South Asian Sub 98 T=0.72 C=0.28, G=0.00
8.3KJPN JAPANESE Study-wide 16760 T=0.66844 C=0.33156
1000Genomes_30x Global Study-wide 6404 T=0.7592 C=0.2408
1000Genomes_30x African Sub 1786 T=0.8147 C=0.1853
1000Genomes_30x Europe Sub 1266 T=0.8341 C=0.1659
1000Genomes_30x South Asian Sub 1202 T=0.6855 C=0.3145
1000Genomes_30x East Asian Sub 1170 T=0.7282 C=0.2718
1000Genomes_30x American Sub 980 T=0.689 C=0.311
1000Genomes Global Study-wide 5008 T=0.7540 C=0.2460
1000Genomes African Sub 1322 T=0.8101 C=0.1899
1000Genomes East Asian Sub 1008 T=0.7192 C=0.2808
1000Genomes Europe Sub 1006 T=0.8260 C=0.1740
1000Genomes South Asian Sub 978 T=0.688 C=0.312
1000Genomes American Sub 694 T=0.686 C=0.314
Genetic variation in the Estonian population Estonian Study-wide 4478 T=0.8289 C=0.1711
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 T=0.8280 C=0.1720
UK 10K study - Twins TWIN COHORT Study-wide 3708 T=0.8358 C=0.1642
KOREAN population from KRGDB KOREAN Study-wide 2930 T=0.7280 C=0.2720
Genome of the Netherlands Release 5 Genome of the Netherlands Study-wide 998 T=0.843 C=0.157
Northern Sweden ACPOP Study-wide 600 T=0.815 C=0.185
Qatari Global Study-wide 216 T=0.741 C=0.259
A Vietnamese Genetic Variation Database Global Study-wide 212 T=0.750 C=0.250
SGDP_PRJ Global Study-wide 204 T=0.441 C=0.559
The Danish reference pan genome Danish Study-wide 40 T=0.72 C=0.28
Siberian Global Study-wide 22 T=0.41 C=0.59
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.41996176T>C
GRCh38.p14 chr 1 NC_000001.11:g.41996176T>G
GRCh37.p13 chr 1 NC_000001.10:g.42461847T>C
GRCh37.p13 chr 1 NC_000001.10:g.42461847T>G
HIVEP3 RefSeqGene NG_030026.2:g.44750A>G
HIVEP3 RefSeqGene NG_030026.2:g.44750A>C
Gene: HIVEP3, HIVEP zinc finger 3 (minus strand)
Molecule type Change Amino acid[Codon] SO Term
HIVEP3 transcript variant 2 NM_001127714.3:c. N/A Genic Upstream Transcript Variant
HIVEP3 transcript variant 1 NM_024503.5:c. N/A Genic Upstream Transcript Variant
HIVEP3 transcript variant 4 NR_038261.2:n. N/A Intron Variant
HIVEP3 transcript variant 3 NR_038260.2:n. N/A Genic Upstream Transcript Variant
HIVEP3 transcript variant X2 XM_011541885.4:c. N/A Genic Upstream Transcript Variant
HIVEP3 transcript variant X3 XM_011541886.4:c. N/A Genic Upstream Transcript Variant
HIVEP3 transcript variant X5 XM_011541887.4:c. N/A Genic Upstream Transcript Variant
HIVEP3 transcript variant X1 XM_047426875.1:c. N/A Genic Upstream Transcript Variant
HIVEP3 transcript variant X4 XM_047426877.1:c. N/A Genic Upstream Transcript Variant
HIVEP3 transcript variant X6 XR_007062478.1:n. N/A Genic Upstream Transcript Variant
HIVEP3 transcript variant X7 XR_007062479.1:n. N/A Genic Upstream Transcript Variant
Gene: LOC124904160, uncharacterized LOC124904160 (plus strand)
Molecule type Change Amino acid[Codon] SO Term
LOC124904160 transcript variant X1 XR_007066031.1: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 T= C G
GRCh38.p14 chr 1 NC_000001.11:g.41996176= NC_000001.11:g.41996176T>C NC_000001.11:g.41996176T>G
GRCh37.p13 chr 1 NC_000001.10:g.42461847= NC_000001.10:g.42461847T>C NC_000001.10:g.42461847T>G
HIVEP3 RefSeqGene NG_030026.2:g.44750= NG_030026.2:g.44750A>G NG_030026.2:g.44750A>C
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#.

54 SubSNP, 18 Frequency submissions
No Submitter Submission ID Date (Build)
1 SC_SNP ss18243018 Feb 28, 2004 (120)
2 GMI ss154918618 Dec 01, 2009 (131)
3 COMPLETE_GENOMICS ss164166479 Jul 04, 2010 (132)
4 COMPLETE_GENOMICS ss166422803 Jul 04, 2010 (132)
5 BCM-HGSC-SUB ss205471931 Jul 04, 2010 (132)
6 1000GENOMES ss230506173 Jul 14, 2010 (132)
7 BL ss253053561 May 09, 2011 (134)
8 GMI ss275797804 May 04, 2012 (137)
9 TISHKOFF ss554027417 Apr 25, 2013 (138)
10 SSMP ss647816970 Apr 25, 2013 (138)
11 EVA-GONL ss975076342 Aug 21, 2014 (142)
12 JMKIDD_LAB ss1067824631 Aug 21, 2014 (142)
13 1000GENOMES ss1290548617 Aug 21, 2014 (142)
14 DDI ss1425783658 Apr 01, 2015 (144)
15 EVA_GENOME_DK ss1574012813 Apr 01, 2015 (144)
16 EVA_DECODE ss1584439072 Apr 01, 2015 (144)
17 EVA_UK10K_ALSPAC ss1599996094 Apr 01, 2015 (144)
18 EVA_UK10K_TWINSUK ss1642990127 Apr 01, 2015 (144)
19 WEILL_CORNELL_DGM ss1918284682 Feb 12, 2016 (147)
20 JJLAB ss2019657182 Sep 14, 2016 (149)
21 USC_VALOUEV ss2147668577 Dec 20, 2016 (150)
22 HUMAN_LONGEVITY ss2161788526 Dec 20, 2016 (150)
23 GRF ss2697577490 Nov 08, 2017 (151)
24 GNOMAD ss2754153585 Nov 08, 2017 (151)
25 SWEGEN ss2986677073 Nov 08, 2017 (151)
26 BIOINF_KMB_FNS_UNIBA ss3023591538 Nov 08, 2017 (151)
27 CSHL ss3343420126 Nov 08, 2017 (151)
28 EGCUT_WGS ss3654742469 Jul 12, 2019 (153)
29 EVA_DECODE ss3686604574 Jul 12, 2019 (153)
30 ACPOP ss3726976111 Jul 12, 2019 (153)
31 EVA ss3746097946 Jul 12, 2019 (153)
32 PACBIO ss3783387972 Jul 12, 2019 (153)
33 PACBIO ss3789050675 Jul 12, 2019 (153)
34 PACBIO ss3793923350 Jul 12, 2019 (153)
35 KHV_HUMAN_GENOMES ss3799111630 Jul 12, 2019 (153)
36 EVA ss3826132391 Apr 25, 2020 (154)
37 EVA ss3836453721 Apr 25, 2020 (154)
38 EVA ss3841859297 Apr 25, 2020 (154)
39 SGDP_PRJ ss3848672395 Apr 25, 2020 (154)
40 KRGDB ss3893645798 Apr 25, 2020 (154)
41 TOPMED ss4446633725 Apr 25, 2021 (155)
42 TOMMO_GENOMICS ss5143543770 Apr 25, 2021 (155)
43 1000G_HIGH_COVERAGE ss5241968781 Oct 13, 2022 (156)
44 EVA ss5318174020 Oct 13, 2022 (156)
45 HUGCELL_USP ss5443065894 Oct 13, 2022 (156)
46 EVA ss5505822518 Oct 13, 2022 (156)
47 1000G_HIGH_COVERAGE ss5514094064 Oct 13, 2022 (156)
48 SANFORD_IMAGENETICS ss5625362894 Oct 13, 2022 (156)
49 TOMMO_GENOMICS ss5668187445 Oct 13, 2022 (156)
50 YY_MCH ss5800522005 Oct 13, 2022 (156)
51 EVA ss5831845346 Oct 13, 2022 (156)
52 EVA ss5848873875 Oct 13, 2022 (156)
53 EVA ss5907914377 Oct 13, 2022 (156)
54 EVA ss5937186480 Oct 13, 2022 (156)
55 1000Genomes NC_000001.10 - 42461847 Oct 11, 2018 (152)
56 1000Genomes_30x NC_000001.11 - 41996176 Oct 13, 2022 (156)
57 The Avon Longitudinal Study of Parents and Children NC_000001.10 - 42461847 Oct 11, 2018 (152)
58 Genetic variation in the Estonian population NC_000001.10 - 42461847 Oct 11, 2018 (152)
59 The Danish reference pan genome NC_000001.10 - 42461847 Apr 25, 2020 (154)
60 gnomAD - Genomes NC_000001.11 - 41996176 Apr 25, 2021 (155)
61 Genome of the Netherlands Release 5 NC_000001.10 - 42461847 Apr 25, 2020 (154)
62 KOREAN population from KRGDB NC_000001.10 - 42461847 Apr 25, 2020 (154)
63 Northern Sweden NC_000001.10 - 42461847 Jul 12, 2019 (153)
64 Qatari NC_000001.10 - 42461847 Apr 25, 2020 (154)
65 SGDP_PRJ NC_000001.10 - 42461847 Apr 25, 2020 (154)
66 Siberian NC_000001.10 - 42461847 Apr 25, 2020 (154)
67 8.3KJPN NC_000001.10 - 42461847 Apr 25, 2021 (155)
68 14KJPN NC_000001.11 - 41996176 Oct 13, 2022 (156)
69 TopMed NC_000001.11 - 41996176 Apr 25, 2021 (155)
70 UK 10K study - Twins NC_000001.10 - 42461847 Oct 11, 2018 (152)
71 A Vietnamese Genetic Variation Database NC_000001.10 - 42461847 Jul 12, 2019 (153)
72 ALFA NC_000001.11 - 41996176 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).

Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
ss164166479, ss166422803, ss205471931, ss253053561, ss275797804, ss1584439072 NC_000001.9:42234433:T:C NC_000001.11:41996175:T:C (self)
1254759, 680646, 480717, 1471843, 290709, 823192, 260976, 326612, 689375, 184931, 1513077, 680646, 139962, ss230506173, ss554027417, ss647816970, ss975076342, ss1067824631, ss1290548617, ss1425783658, ss1574012813, ss1599996094, ss1642990127, ss1918284682, ss2019657182, ss2147668577, ss2697577490, ss2754153585, ss2986677073, ss3343420126, ss3654742469, ss3726976111, ss3746097946, ss3783387972, ss3789050675, ss3793923350, ss3826132391, ss3836453721, ss3848672395, ss3893645798, ss5143543770, ss5318174020, ss5505822518, ss5625362894, ss5831845346, ss5937186480 NC_000001.10:42461846:T:C NC_000001.11:41996175:T:C (self)
1619999, 8836521, 2024549, 10240060, 2078206555, ss2161788526, ss3023591538, ss3686604574, ss3799111630, ss3841859297, ss4446633725, ss5241968781, ss5443065894, ss5514094064, ss5668187445, ss5800522005, ss5848873875, ss5907914377 NC_000001.11:41996175:T:C NC_000001.11:41996175:T:C (self)
ss18243018 NT_032977.6:4068293:T:C NC_000001.11:41996175:T:C (self)
ss154918618 NT_032977.9:12433764:T:C NC_000001.11:41996175:T:C (self)
2078206555 NC_000001.11:41996175:T:G NC_000001.11:41996175:T: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 rs12116430

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