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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.

rs6045449

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr20:18537258 (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
A>G
Variation Type
SNV Single Nucleotide Variation
Frequency
G=0.138097 (36553/264690, TOPMED)
G=0.131653 (18368/139518, GnomAD)
G=0.13412 (3790/28258, 14KJPN) (+ 10 more)
G=0.12500 (2315/18520, ALFA)
G=0.13365 (2240/16760, 8.3KJPN)
G=0.1195 (765/6404, 1000G_30x)
G=0.1196 (599/5008, 1000G)
G=0.1591 (465/2922, KOREAN)
G=0.104 (104/998, GoNL)
G=0.083 (50/600, NorthernSweden)
G=0.134 (29/216, Qatari)
A=0.459 (68/148, SGDP_PRJ)
G=0.17 (7/40, GENOME_DK)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
SEC23B : 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 18520 A=0.87500 G=0.12500
European Sub 14152 A=0.88348 G=0.11652
African Sub 2898 A=0.8596 G=0.1404
African Others Sub 114 A=0.825 G=0.175
African American Sub 2784 A=0.8610 G=0.1390
Asian Sub 112 A=0.875 G=0.125
East Asian Sub 86 A=0.86 G=0.14
Other Asian Sub 26 A=0.92 G=0.08
Latin American 1 Sub 146 A=0.822 G=0.178
Latin American 2 Sub 610 A=0.772 G=0.228
South Asian Sub 98 A=0.95 G=0.05
Other Sub 504 A=0.851 G=0.149


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 A=0.861903 G=0.138097
gnomAD - Genomes Global Study-wide 139518 A=0.868347 G=0.131653
gnomAD - Genomes European Sub 75692 A=0.88015 G=0.11985
gnomAD - Genomes African Sub 41714 A=0.87057 G=0.12943
gnomAD - Genomes American Sub 13560 A=0.81276 G=0.18724
gnomAD - Genomes Ashkenazi Jewish Sub 3316 A=0.8350 G=0.1650
gnomAD - Genomes East Asian Sub 3096 A=0.8324 G=0.1676
gnomAD - Genomes Other Sub 2140 A=0.8636 G=0.1364
14KJPN JAPANESE Study-wide 28258 A=0.86588 G=0.13412
Allele Frequency Aggregator Total Global 18520 A=0.87500 G=0.12500
Allele Frequency Aggregator European Sub 14152 A=0.88348 G=0.11652
Allele Frequency Aggregator African Sub 2898 A=0.8596 G=0.1404
Allele Frequency Aggregator Latin American 2 Sub 610 A=0.772 G=0.228
Allele Frequency Aggregator Other Sub 504 A=0.851 G=0.149
Allele Frequency Aggregator Latin American 1 Sub 146 A=0.822 G=0.178
Allele Frequency Aggregator Asian Sub 112 A=0.875 G=0.125
Allele Frequency Aggregator South Asian Sub 98 A=0.95 G=0.05
8.3KJPN JAPANESE Study-wide 16760 A=0.86635 G=0.13365
1000Genomes_30x Global Study-wide 6404 A=0.8805 G=0.1195
1000Genomes_30x African Sub 1786 A=0.8667 G=0.1333
1000Genomes_30x Europe Sub 1266 A=0.8902 G=0.1098
1000Genomes_30x South Asian Sub 1202 A=0.9684 G=0.0316
1000Genomes_30x East Asian Sub 1170 A=0.8427 G=0.1573
1000Genomes_30x American Sub 980 A=0.831 G=0.169
1000Genomes Global Study-wide 5008 A=0.8804 G=0.1196
1000Genomes African Sub 1322 A=0.8631 G=0.1369
1000Genomes East Asian Sub 1008 A=0.8403 G=0.1597
1000Genomes Europe Sub 1006 A=0.8887 G=0.1113
1000Genomes South Asian Sub 978 A=0.969 G=0.031
1000Genomes American Sub 694 A=0.834 G=0.166
KOREAN population from KRGDB KOREAN Study-wide 2922 A=0.8409 G=0.1591
Genome of the Netherlands Release 5 Genome of the Netherlands Study-wide 998 A=0.896 G=0.104
Northern Sweden ACPOP Study-wide 600 A=0.917 G=0.083
Qatari Global Study-wide 216 A=0.866 G=0.134
SGDP_PRJ Global Study-wide 148 A=0.459 G=0.541
The Danish reference pan genome Danish Study-wide 40 A=0.82 G=0.17
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 20 NC_000020.11:g.18537258A>G
GRCh37.p13 chr 20 NC_000020.10:g.18517902A>G
SEC23B RefSeqGene (LRG_1134) NG_016281.2:g.34777A>G
Gene: SEC23B, SEC23 homolog B, COPII coat complex component (plus strand)
Molecule type Change Amino acid[Codon] SO Term
SEC23B transcript variant 4 NM_001172745.3:c.1404+151…

NM_001172745.3:c.1404+1516A>G

N/A Intron Variant
SEC23B transcript variant 5 NM_001172746.3:c.1350+151…

NM_001172746.3:c.1350+1516A>G

N/A Intron Variant
SEC23B transcript variant 1 NM_006363.6:c.1404+1516A>G N/A Intron Variant
SEC23B transcript variant 2 NM_032985.6:c.1404+1516A>G N/A Intron Variant
SEC23B transcript variant 3 NM_032986.5:c.1404+1516A>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 A= G
GRCh38.p14 chr 20 NC_000020.11:g.18537258= NC_000020.11:g.18537258A>G
GRCh37.p13 chr 20 NC_000020.10:g.18517902= NC_000020.10:g.18517902A>G
SEC23B RefSeqGene (LRG_1134) NG_016281.2:g.34777= NG_016281.2:g.34777A>G
SEC23B transcript variant 4 NM_001172745.1:c.1404+1516= NM_001172745.1:c.1404+1516A>G
SEC23B transcript variant 4 NM_001172745.3:c.1404+1516= NM_001172745.3:c.1404+1516A>G
SEC23B transcript variant 5 NM_001172746.1:c.1350+1516= NM_001172746.1:c.1350+1516A>G
SEC23B transcript variant 5 NM_001172746.3:c.1350+1516= NM_001172746.3:c.1350+1516A>G
SEC23B transcript variant 1 NM_006363.4:c.1404+1516= NM_006363.4:c.1404+1516A>G
SEC23B transcript variant 1 NM_006363.6:c.1404+1516= NM_006363.6:c.1404+1516A>G
SEC23B transcript variant 2 NM_032985.4:c.1404+1516= NM_032985.4:c.1404+1516A>G
SEC23B transcript variant 2 NM_032985.6:c.1404+1516= NM_032985.6:c.1404+1516A>G
SEC23B transcript variant 3 NM_032986.3:c.1404+1516= NM_032986.3:c.1404+1516A>G
SEC23B transcript variant 3 NM_032986.5:c.1404+1516= NM_032986.5:c.1404+1516A>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#.

46 SubSNP, 13 Frequency submissions
No Submitter Submission ID Date (Build)
1 SC_SNP ss8356074 Apr 21, 2003 (114)
2 SC_SNP ss11106019 Jul 11, 2003 (123)
3 CSHL-HAPMAP ss20121461 Feb 27, 2004 (123)
4 SSAHASNP ss21796803 Apr 05, 2004 (123)
5 ABI ss41439354 Mar 16, 2006 (126)
6 BCMHGSC_JDW ss91658839 Mar 24, 2008 (129)
7 HUMANGENOME_JCVI ss96220724 Feb 05, 2009 (130)
8 ENSEMBL ss135750637 Dec 01, 2009 (147)
9 COMPLETE_GENOMICS ss169261933 Jul 04, 2010 (132)
10 BUSHMAN ss203850133 Jul 04, 2010 (132)
11 BCM-HGSC-SUB ss208765109 Jul 04, 2010 (132)
12 GMI ss283324497 May 04, 2012 (137)
13 PJP ss292625086 May 09, 2011 (134)
14 1000GENOMES ss340656334 May 09, 2011 (134)
15 TISHKOFF ss566174850 Apr 25, 2013 (138)
16 SSMP ss662049684 Apr 25, 2013 (138)
17 EVA-GONL ss994604697 Aug 21, 2014 (142)
18 1000GENOMES ss1364299940 Aug 21, 2014 (142)
19 EVA_GENOME_DK ss1579464264 Apr 01, 2015 (144)
20 HAMMER_LAB ss1809449480 Sep 08, 2015 (146)
21 WEILL_CORNELL_DGM ss1938112265 Feb 12, 2016 (147)
22 JJLAB ss2029840465 Sep 14, 2016 (149)
23 HUMAN_LONGEVITY ss2241816008 Dec 20, 2016 (150)
24 SYSTEMSBIOZJU ss2629415989 Nov 08, 2017 (151)
25 GRF ss2704068270 Nov 08, 2017 (151)
26 GNOMAD ss2966089110 Nov 08, 2017 (151)
27 SWEGEN ss3017963808 Nov 08, 2017 (151)
28 CSHL ss3352449365 Nov 08, 2017 (151)
29 URBANLAB ss3650985322 Oct 12, 2018 (152)
30 ACPOP ss3743303091 Jul 13, 2019 (153)
31 EVA ss3758498380 Jul 13, 2019 (153)
32 KHV_HUMAN_GENOMES ss3821668644 Jul 13, 2019 (153)
33 SGDP_PRJ ss3888856292 Apr 27, 2020 (154)
34 KRGDB ss3939056842 Apr 27, 2020 (154)
35 TOPMED ss5084318540 Apr 27, 2021 (155)
36 TOMMO_GENOMICS ss5229103017 Apr 27, 2021 (155)
37 1000G_HIGH_COVERAGE ss5308289503 Oct 16, 2022 (156)
38 EVA ss5436639606 Oct 16, 2022 (156)
39 EVA ss5512176418 Oct 16, 2022 (156)
40 1000G_HIGH_COVERAGE ss5614475838 Oct 16, 2022 (156)
41 SANFORD_IMAGENETICS ss5662983157 Oct 16, 2022 (156)
42 TOMMO_GENOMICS ss5788163377 Oct 16, 2022 (156)
43 YY_MCH ss5817869252 Oct 16, 2022 (156)
44 EVA ss5845528484 Oct 16, 2022 (156)
45 EVA ss5922913154 Oct 16, 2022 (156)
46 EVA ss5957894035 Oct 16, 2022 (156)
47 1000Genomes NC_000020.10 - 18517902 Oct 12, 2018 (152)
48 1000Genomes_30x NC_000020.11 - 18537258 Oct 16, 2022 (156)
49 The Danish reference pan genome NC_000020.10 - 18517902 Apr 27, 2020 (154)
50 gnomAD - Genomes NC_000020.11 - 18537258 Apr 27, 2021 (155)
51 Genome of the Netherlands Release 5 NC_000020.10 - 18517902 Apr 27, 2020 (154)
52 KOREAN population from KRGDB NC_000020.10 - 18517902 Apr 27, 2020 (154)
53 Northern Sweden NC_000020.10 - 18517902 Jul 13, 2019 (153)
54 Qatari NC_000020.10 - 18517902 Apr 27, 2020 (154)
55 SGDP_PRJ NC_000020.10 - 18517902 Apr 27, 2020 (154)
56 8.3KJPN NC_000020.10 - 18517902 Apr 27, 2021 (155)
57 14KJPN NC_000020.11 - 18537258 Oct 16, 2022 (156)
58 TopMed NC_000020.11 - 18537258 Apr 27, 2021 (155)
59 ALFA NC_000020.11 - 18537258 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).

Associated ID History Updated (Build)
rs7344420 Oct 07, 2004 (123)
rs36156952 Oct 14, 2006 (127)
rs76754200 Jul 19, 2016 (147)
Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
ss91658839, ss169261933, ss203850133, ss208765109, ss283324497, ss292625086 NC_000020.9:18465901:A:G NC_000020.11:18537257:A:G (self)
77747805, 5629203, 19181632, 46234236, 16587956, 20154187, 40873272, 87072324, ss340656334, ss566174850, ss662049684, ss994604697, ss1364299940, ss1579464264, ss1809449480, ss1938112265, ss2029840465, ss2629415989, ss2704068270, ss2966089110, ss3017963808, ss3352449365, ss3743303091, ss3758498380, ss3888856292, ss3939056842, ss5229103017, ss5436639606, ss5512176418, ss5662983157, ss5845528484, ss5957894035 NC_000020.10:18517901:A:G NC_000020.11:18537257:A:G (self)
102001773, 548157932, 122000481, 359427485, 11663780691, ss2241816008, ss3650985322, ss3821668644, ss5084318540, ss5308289503, ss5614475838, ss5788163377, ss5817869252, ss5922913154 NC_000020.11:18537257:A:G NC_000020.11:18537257:A:G (self)
ss8356074, ss11106019, ss20121461, ss21796803, ss41439354, ss96220724, ss135750637 NT_011387.8:18457901:A:G NC_000020.11:18537257:A: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 rs6045449

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