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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.

rs12749112

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr1:52970891 (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=0.021059 (5574/264690, TOPMED)
C=0.024078 (3359/139504, GnomAD)
C=0.03071 (2097/68282, ALFA) (+ 14 more)
C=0.0111 (71/6404, 1000G_30x)
C=0.0110 (55/5008, 1000G)
C=0.0509 (228/4480, Estonian)
C=0.0311 (120/3854, ALSPAC)
C=0.0334 (124/3708, TWINSUK)
C=0.0053 (11/2084, HGDP_Stanford)
C=0.0053 (6/1122, Daghestan)
C=0.021 (21/998, GoNL)
C=0.020 (18/880, HapMap)
C=0.048 (29/600, NorthernSweden)
C=0.07 (3/40, GENOME_DK)
C=0.00 (0/20, Ancient Sardinia)
T=0.5 (4/8, SGDP_PRJ)
C=0.5 (4/8, SGDP_PRJ)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
SCP2 : 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 68282 T=0.96929 C=0.03071
European Sub 55660 T=0.96484 C=0.03516
African Sub 4530 T=0.9914 C=0.0086
African Others Sub 170 T=1.000 C=0.000
African American Sub 4360 T=0.9911 C=0.0089
Asian Sub 192 T=1.000 C=0.000
East Asian Sub 150 T=1.000 C=0.000
Other Asian Sub 42 T=1.00 C=0.00
Latin American 1 Sub 254 T=0.984 C=0.016
Latin American 2 Sub 1232 T=0.9773 C=0.0227
South Asian Sub 4954 T=0.9917 C=0.0083
Other Sub 1460 T=0.9808 C=0.0192


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=0.978941 C=0.021059
gnomAD - Genomes Global Study-wide 139504 T=0.975922 C=0.024078
gnomAD - Genomes European Sub 75450 T=0.96387 C=0.03613
gnomAD - Genomes African Sub 41896 T=0.99403 C=0.00597
gnomAD - Genomes American Sub 13574 T=0.98401 C=0.01599
gnomAD - Genomes Ashkenazi Jewish Sub 3322 T=0.9666 C=0.0334
gnomAD - Genomes East Asian Sub 3124 T=1.0000 C=0.0000
gnomAD - Genomes Other Sub 2138 T=0.9743 C=0.0257
Allele Frequency Aggregator Total Global 68282 T=0.96929 C=0.03071
Allele Frequency Aggregator European Sub 55660 T=0.96484 C=0.03516
Allele Frequency Aggregator South Asian Sub 4954 T=0.9917 C=0.0083
Allele Frequency Aggregator African Sub 4530 T=0.9914 C=0.0086
Allele Frequency Aggregator Other Sub 1460 T=0.9808 C=0.0192
Allele Frequency Aggregator Latin American 2 Sub 1232 T=0.9773 C=0.0227
Allele Frequency Aggregator Latin American 1 Sub 254 T=0.984 C=0.016
Allele Frequency Aggregator Asian Sub 192 T=1.000 C=0.000
1000Genomes_30x Global Study-wide 6404 T=0.9889 C=0.0111
1000Genomes_30x African Sub 1786 T=0.9989 C=0.0011
1000Genomes_30x Europe Sub 1266 T=0.9613 C=0.0387
1000Genomes_30x South Asian Sub 1202 T=0.9942 C=0.0058
1000Genomes_30x East Asian Sub 1170 T=1.0000 C=0.0000
1000Genomes_30x American Sub 980 T=0.987 C=0.013
1000Genomes Global Study-wide 5008 T=0.9890 C=0.0110
1000Genomes African Sub 1322 T=0.9977 C=0.0023
1000Genomes East Asian Sub 1008 T=1.0000 C=0.0000
1000Genomes Europe Sub 1006 T=0.9642 C=0.0358
1000Genomes South Asian Sub 978 T=0.993 C=0.007
1000Genomes American Sub 694 T=0.987 C=0.013
Genetic variation in the Estonian population Estonian Study-wide 4480 T=0.9491 C=0.0509
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 T=0.9689 C=0.0311
UK 10K study - Twins TWIN COHORT Study-wide 3708 T=0.9666 C=0.0334
HGDP-CEPH-db Supplement 1 Global Study-wide 2084 T=0.9947 C=0.0053
HGDP-CEPH-db Supplement 1 Est_Asia Sub 470 T=1.000 C=0.000
HGDP-CEPH-db Supplement 1 Central_South_Asia Sub 414 T=0.998 C=0.002
HGDP-CEPH-db Supplement 1 Middle_Est Sub 350 T=1.000 C=0.000
HGDP-CEPH-db Supplement 1 Europe Sub 320 T=0.969 C=0.031
HGDP-CEPH-db Supplement 1 Africa Sub 242 T=1.000 C=0.000
HGDP-CEPH-db Supplement 1 America Sub 216 T=1.000 C=0.000
HGDP-CEPH-db Supplement 1 Oceania Sub 72 T=1.00 C=0.00
Genome-wide autozygosity in Daghestan Global Study-wide 1122 T=0.9947 C=0.0053
Genome-wide autozygosity in Daghestan Daghestan Sub 616 T=0.997 C=0.003
Genome-wide autozygosity in Daghestan Near_East Sub 142 T=1.000 C=0.000
Genome-wide autozygosity in Daghestan Central Asia Sub 122 T=1.000 C=0.000
Genome-wide autozygosity in Daghestan Europe Sub 108 T=0.972 C=0.028
Genome-wide autozygosity in Daghestan South Asian Sub 98 T=1.00 C=0.00
Genome-wide autozygosity in Daghestan Caucasus Sub 36 T=0.97 C=0.03
Genome of the Netherlands Release 5 Genome of the Netherlands Study-wide 998 T=0.979 C=0.021
HapMap Global Study-wide 880 T=0.980 C=0.020
HapMap American Sub 502 T=0.974 C=0.026
HapMap Europe Sub 176 T=0.972 C=0.028
HapMap African Sub 114 T=1.000 C=0.000
HapMap Asian Sub 88 T=1.00 C=0.00
Northern Sweden ACPOP Study-wide 600 T=0.952 C=0.048
The Danish reference pan genome Danish Study-wide 40 T=0.93 C=0.07
Ancient Sardinia genome-wide 1240k capture data generation and analysis Global Study-wide 20 T=1.00 C=0.00
SGDP_PRJ 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 1 NC_000001.11:g.52970891T>C
GRCh37.p13 chr 1 NC_000001.10:g.53436563T>C
SCP2 RefSeqGene NG_012211.1:g.48616T>C
Gene: SCP2, sterol carrier protein 2 (plus strand)
Molecule type Change Amino acid[Codon] SO Term
SCP2 transcript variant 2 NM_001007098.3:c.392-3878…

NM_001007098.3:c.392-3878T>C

N/A Intron Variant
SCP2 transcript variant 7 NM_001193599.2:c.452-3878…

NM_001193599.2:c.452-3878T>C

N/A Intron Variant
SCP2 transcript variant 6 NM_001193600.2:c.392-3878…

NM_001193600.2:c.392-3878T>C

N/A Intron Variant
SCP2 transcript variant 8 NM_001193617.2:c.281-3878…

NM_001193617.2:c.281-3878T>C

N/A Intron Variant
SCP2 transcript variant 9 NM_001330587.2:c.524-3878…

NM_001330587.2:c.524-3878T>C

N/A Intron Variant
SCP2 transcript variant 1 NM_002979.5:c.524-3878T>C N/A Intron Variant
SCP2 transcript variant 3 NM_001007099.3:c. N/A Genic Upstream Transcript Variant
SCP2 transcript variant 4 NM_001007100.3:c. N/A Genic Upstream Transcript Variant
SCP2 transcript variant 5 NM_001007250.3:c. N/A Genic Upstream Transcript Variant
SCP2 transcript variant X2 XM_005271103.5:c.524-3878…

XM_005271103.5:c.524-3878T>C

N/A Intron Variant
SCP2 transcript variant X5 XM_011541935.3:c.524-3878…

XM_011541935.3:c.524-3878T>C

N/A Intron Variant
SCP2 transcript variant X1 XM_047427504.1:c.524-3878…

XM_047427504.1:c.524-3878T>C

N/A Intron Variant
SCP2 transcript variant X3 XM_047427506.1:c.524-3878…

XM_047427506.1:c.524-3878T>C

N/A Intron Variant
SCP2 transcript variant X4 XM_047427507.1:c.524-3878…

XM_047427507.1:c.524-3878T>C

N/A Intron Variant
SCP2 transcript variant X6 XM_047427508.1:c.392-3878…

XM_047427508.1:c.392-3878T>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 T= C
GRCh38.p14 chr 1 NC_000001.11:g.52970891= NC_000001.11:g.52970891T>C
GRCh37.p13 chr 1 NC_000001.10:g.53436563= NC_000001.10:g.53436563T>C
SCP2 RefSeqGene NG_012211.1:g.48616= NG_012211.1:g.48616T>C
SCP2 transcript variant 2 NM_001007098.2:c.392-3878= NM_001007098.2:c.392-3878T>C
SCP2 transcript variant 2 NM_001007098.3:c.392-3878= NM_001007098.3:c.392-3878T>C
SCP2 transcript variant 7 NM_001193599.1:c.452-3878= NM_001193599.1:c.452-3878T>C
SCP2 transcript variant 7 NM_001193599.2:c.452-3878= NM_001193599.2:c.452-3878T>C
SCP2 transcript variant 6 NM_001193600.1:c.392-3878= NM_001193600.1:c.392-3878T>C
SCP2 transcript variant 6 NM_001193600.2:c.392-3878= NM_001193600.2:c.392-3878T>C
SCP2 transcript variant 8 NM_001193617.1:c.281-3878= NM_001193617.1:c.281-3878T>C
SCP2 transcript variant 8 NM_001193617.2:c.281-3878= NM_001193617.2:c.281-3878T>C
SCP2 transcript variant 9 NM_001330587.2:c.524-3878= NM_001330587.2:c.524-3878T>C
SCP2 transcript variant 1 NM_002979.4:c.524-3878= NM_002979.4:c.524-3878T>C
SCP2 transcript variant 1 NM_002979.5:c.524-3878= NM_002979.5:c.524-3878T>C
SCP2 transcript variant X1 XM_005271103.1:c.524-3878= XM_005271103.1:c.524-3878T>C
SCP2 transcript variant X2 XM_005271103.5:c.524-3878= XM_005271103.5:c.524-3878T>C
SCP2 transcript variant X2 XM_005271104.1:c.524-3878= XM_005271104.1:c.524-3878T>C
SCP2 transcript variant X5 XM_011541935.3:c.524-3878= XM_011541935.3:c.524-3878T>C
SCP2 transcript variant X1 XM_047427504.1:c.524-3878= XM_047427504.1:c.524-3878T>C
SCP2 transcript variant X3 XM_047427506.1:c.524-3878= XM_047427506.1:c.524-3878T>C
SCP2 transcript variant X4 XM_047427507.1:c.524-3878= XM_047427507.1:c.524-3878T>C
SCP2 transcript variant X6 XM_047427508.1:c.392-3878= XM_047427508.1:c.392-3878T>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#.

58 SubSNP, 16 Frequency submissions
No Submitter Submission ID Date (Build)
1 SSAHASNP ss20556276 Apr 05, 2004 (121)
2 ABI ss44074869 Mar 15, 2006 (126)
3 ILLUMINA ss67037562 Nov 30, 2006 (127)
4 ILLUMINA ss67361655 Nov 30, 2006 (127)
5 ILLUMINA ss68138318 Dec 12, 2006 (127)
6 ILLUMINA ss70583888 May 26, 2008 (130)
7 ILLUMINA ss71126539 May 17, 2007 (127)
8 ILLUMINA ss75565183 Dec 06, 2007 (129)
9 KRIBB_YJKIM ss85270019 Dec 16, 2007 (130)
10 HUMANGENOME_JCVI ss99207480 Feb 06, 2009 (130)
11 1000GENOMES ss108192576 Jan 23, 2009 (130)
12 ENSEMBL ss138945449 Dec 01, 2009 (131)
13 ILLUMINA ss153278174 Dec 01, 2009 (131)
14 ILLUMINA ss159233679 Dec 01, 2009 (131)
15 ILLUMINA ss172238617 Jul 04, 2010 (132)
16 1000GENOMES ss230528277 Jul 14, 2010 (132)
17 ILLUMINA ss244277588 Jul 04, 2010 (132)
18 PJP ss290508320 May 09, 2011 (134)
19 ILLUMINA ss536812177 Sep 08, 2015 (146)
20 ILLUMINA ss832746016 Jul 12, 2019 (153)
21 EVA-GONL ss975144837 Aug 21, 2014 (142)
22 1000GENOMES ss1290834051 Aug 21, 2014 (142)
23 HAMMER_LAB ss1397245043 Sep 08, 2015 (146)
24 EVA_GENOME_DK ss1574048796 Apr 01, 2015 (144)
25 EVA_DECODE ss1584510704 Apr 01, 2015 (144)
26 EVA_UK10K_ALSPAC ss1600142443 Apr 01, 2015 (144)
27 EVA_UK10K_TWINSUK ss1643136476 Apr 01, 2015 (144)
28 JJLAB ss2019691328 Sep 14, 2016 (149)
29 ILLUMINA ss2094958462 Dec 20, 2016 (150)
30 HUMAN_LONGEVITY ss2162385714 Dec 20, 2016 (150)
31 GNOMAD ss2754992571 Nov 08, 2017 (151)
32 SWEGEN ss2986793410 Nov 08, 2017 (151)
33 ILLUMINA ss3626093740 Oct 11, 2018 (152)
34 ILLUMINA ss3637755730 Oct 11, 2018 (152)
35 ILLUMINA ss3638896793 Oct 11, 2018 (152)
36 ILLUMINA ss3639760790 Oct 11, 2018 (152)
37 ILLUMINA ss3642768003 Oct 11, 2018 (152)
38 ILLUMINA ss3643814543 Oct 11, 2018 (152)
39 URBANLAB ss3646659679 Oct 11, 2018 (152)
40 ILLUMINA ss3651412510 Oct 11, 2018 (152)
41 EGCUT_WGS ss3654856775 Jul 12, 2019 (153)
42 EVA_DECODE ss3686742205 Jul 12, 2019 (153)
43 ACPOP ss3727033589 Jul 12, 2019 (153)
44 HGDP ss3847332622 Apr 25, 2020 (154)
45 SGDP_PRJ ss3848815544 Apr 25, 2020 (154)
46 EVA ss3984794913 Apr 25, 2021 (155)
47 EVA ss4016909389 Apr 25, 2021 (155)
48 TOPMED ss4449257092 Apr 25, 2021 (155)
49 1000G_HIGH_COVERAGE ss5242218861 Oct 17, 2022 (156)
50 EVA ss5318630362 Oct 17, 2022 (156)
51 HUGCELL_USP ss5443285354 Oct 17, 2022 (156)
52 1000G_HIGH_COVERAGE ss5514471104 Oct 17, 2022 (156)
53 SANFORD_IMAGENETICS ss5624204432 Oct 17, 2022 (156)
54 SANFORD_IMAGENETICS ss5625499687 Oct 17, 2022 (156)
55 EVA ss5831938697 Oct 17, 2022 (156)
56 EVA ss5908199926 Oct 17, 2022 (156)
57 EVA ss5937330005 Oct 17, 2022 (156)
58 EVA ss5979273329 Oct 17, 2022 (156)
59 1000Genomes NC_000001.10 - 53436563 Oct 11, 2018 (152)
60 1000Genomes_30x NC_000001.11 - 52970891 Oct 17, 2022 (156)
61 The Avon Longitudinal Study of Parents and Children NC_000001.10 - 53436563 Oct 11, 2018 (152)
62 Genome-wide autozygosity in Daghestan NC_000001.9 - 53209151 Apr 25, 2020 (154)
63 Genetic variation in the Estonian population NC_000001.10 - 53436563 Oct 11, 2018 (152)
64 The Danish reference pan genome NC_000001.10 - 53436563 Apr 25, 2020 (154)
65 gnomAD - Genomes NC_000001.11 - 52970891 Apr 25, 2021 (155)
66 Genome of the Netherlands Release 5 NC_000001.10 - 53436563 Apr 25, 2020 (154)
67 HGDP-CEPH-db Supplement 1 NC_000001.9 - 53209151 Apr 25, 2020 (154)
68 HapMap NC_000001.11 - 52970891 Apr 25, 2020 (154)
69 Northern Sweden NC_000001.10 - 53436563 Jul 12, 2019 (153)
70 Ancient Sardinia genome-wide 1240k capture data generation and analysis NC_000001.10 - 53436563 Apr 25, 2021 (155)
71 SGDP_PRJ NC_000001.10 - 53436563 Apr 25, 2020 (154)
72 TopMed NC_000001.11 - 52970891 Apr 25, 2021 (155)
73 UK 10K study - Twins NC_000001.10 - 53436563 Oct 11, 2018 (152)
74 ALFA NC_000001.11 - 52970891 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)
rs61071553 May 26, 2008 (130)
Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
ss3638896793, ss3639760790, ss3643814543 NC_000001.8:53148583:T:C NC_000001.11:52970890:T:C (self)
6475, 10514, ss108192576, ss290508320, ss1397245043, ss1584510704, ss3642768003, ss3847332622 NC_000001.9:53209150:T:C NC_000001.11:52970890:T:C (self)
1550410, 842485, 595023, 1495374, 356777, 318454, 20840, 832524, 842485, ss230528277, ss536812177, ss832746016, ss975144837, ss1290834051, ss1574048796, ss1600142443, ss1643136476, ss2019691328, ss2094958462, ss2754992571, ss2986793410, ss3626093740, ss3637755730, ss3651412510, ss3654856775, ss3727033589, ss3848815544, ss3984794913, ss4016909389, ss5318630362, ss5624204432, ss5625499687, ss5831938697, ss5937330005, ss5979273329 NC_000001.10:53436562:T:C NC_000001.11:52970890:T:C (self)
1997039, 10997623, 64989, 12863427, 10675681734, ss2162385714, ss3646659679, ss3686742205, ss4449257092, ss5242218861, ss5443285354, ss5514471104, ss5908199926 NC_000001.11:52970890:T:C NC_000001.11:52970890:T:C (self)
ss20556276 NT_032977.6:14999633:T:C NC_000001.11:52970890:T:C (self)
ss44074869, ss67037562, ss67361655, ss68138318, ss70583888, ss71126539, ss75565183, ss85270019, ss99207480, ss138945449, ss153278174, ss159233679, ss172238617, ss244277588 NT_032977.9:23408480:T:C NC_000001.11:52970890: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 rs12749112

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