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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.

rs28440105

Current Build 155

Released April 9, 2021

Organism
Homo sapiens
Position
chr11:5248569 (GRCh38.p13) 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>C / A>T
Variation Type
SNV Single Nucleotide Variation
Frequency
A=0.168046 (44480/264690, TOPMED)
A=0.184770 (25506/138042, GnomAD)
A=0.16183 (2712/16758, 8.3KJPN) (+ 11 more)
A=0.2699 (1904/7054, ALFA)
A=0.1573 (788/5008, 1000G)
A=0.1249 (366/2930, KOREAN)
A=0.1053 (193/1832, Korea1K)
A=0.210 (126/600, NorthernSweden)
A=0.102 (55/540, SGDP_PRJ)
C=0.109 (58/534, MGP)
A=0.255 (55/216, Qatari)
A=0.12 (5/40, GENOME_DK)
A=0.50 (8/16, Siberian)
C=0.50 (8/16, Siberian)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
HBG1 : Intron Variant
Publications
4 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: 20201027095038
Population Group Sample Size Ref Allele Alt Allele
Total Global 7054 A=0.2699 C=0.7301, T=0.0000
European Sub 6846 A=0.2629 C=0.7371, T=0.0000
African Sub 118 A=0.415 C=0.585, T=0.000
African Others Sub 8 A=0.2 C=0.8, T=0.0
African American Sub 110 A=0.427 C=0.573, T=0.000
Asian Sub 4 A=0.0 C=1.0, T=0.0
East Asian Sub 2 A=0.0 C=1.0, T=0.0
Other Asian Sub 2 A=0.0 C=1.0, T=0.0
Latin American 1 Sub 4 A=1.0 C=0.0, T=0.0
Latin American 2 Sub 24 A=1.00 C=0.00, T=0.00
South Asian Sub 6 A=0.3 C=0.7, T=0.0
Other Sub 52 A=0.48 C=0.52, T=0.00


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=0.168046 C=0.831954
gnomAD - Genomes Global Study-wide 138042 A=0.184770 C=0.815230
gnomAD - Genomes European Sub 75658 A=0.22501 C=0.77499
gnomAD - Genomes African Sub 40268 A=0.13005 C=0.86995
gnomAD - Genomes American Sub 13562 A=0.15352 C=0.84648
gnomAD - Genomes Ashkenazi Jewish Sub 3302 A=0.1623 C=0.8377
gnomAD - Genomes East Asian Sub 3118 A=0.0946 C=0.9054
gnomAD - Genomes Other Sub 2134 A=0.1556 C=0.8444
8.3KJPN JAPANESE Study-wide 16758 A=0.16183 C=0.83817
1000Genomes Global Study-wide 5008 A=0.1573 C=0.8427
1000Genomes African Sub 1322 A=0.1218 C=0.8782
1000Genomes East Asian Sub 1008 A=0.1121 C=0.8879
1000Genomes Europe Sub 1006 A=0.2197 C=0.7803
1000Genomes South Asian Sub 978 A=0.175 C=0.825
1000Genomes American Sub 694 A=0.176 C=0.824
KOREAN population from KRGDB KOREAN Study-wide 2930 A=0.1249 C=0.8751
Korean Genome Project KOREAN Study-wide 1832 A=0.1053 C=0.8947
Northern Sweden ACPOP Study-wide 600 A=0.210 C=0.790
SGDP_PRJ Global Study-wide 540 A=0.102 C=0.898
Medical Genome Project healthy controls from Spanish population Spanish controls Study-wide 534 A=0.891 C=0.109
Qatari Global Study-wide 216 A=0.255 C=0.745
The Danish reference pan genome Danish Study-wide 40 A=0.12 C=0.88
Siberian Global Study-wide 16 A=0.50 C=0.50
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.p13 chr 11 NC_000011.10:g.5248569A>C
GRCh38.p13 chr 11 NC_000011.10:g.5248569A>T
GRCh37.p13 chr 11 NC_000011.9:g.5269799A>C
GRCh37.p13 chr 11 NC_000011.9:g.5269799A>T
HBB region RefSeqGene NG_000007.3:g.49047T>G
HBB region RefSeqGene NG_000007.3:g.49047T>A
HBD RefSeqGene (LRG_1335) NG_063112.2:g.89T>G
HBD RefSeqGene (LRG_1335) NG_063112.2:g.89T>A
Gene: HBG1, hemoglobin subunit gamma 1 (minus strand)
Molecule type Change Amino acid[Codon] SO Term
HBG1 transcript NM_000559.3:c.316-82T>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= C T
GRCh38.p13 chr 11 NC_000011.10:g.5248569= NC_000011.10:g.5248569A>C NC_000011.10:g.5248569A>T
GRCh37.p13 chr 11 NC_000011.9:g.5269799= NC_000011.9:g.5269799A>C NC_000011.9:g.5269799A>T
HBB region RefSeqGene NG_000007.3:g.49047= NG_000007.3:g.49047T>G NG_000007.3:g.49047T>A
HBD RefSeqGene (LRG_1335) NG_063112.2:g.89= NG_063112.2:g.89T>G NG_063112.2:g.89T>A
HBG1 transcript NM_000559.2:c.316-82= NM_000559.2:c.316-82T>G NM_000559.2:c.316-82T>A
HBG1 transcript NM_000559.3:c.316-82= NM_000559.3:c.316-82T>G NM_000559.3:c.316-82T>A
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#.

52 SubSNP, 13 Frequency submissions
No Submitter Submission ID Date (Build)
1 SC_JCM ss11300756 Apr 01, 2015 (144)
2 WI_SSAHASNP ss12172269 Apr 01, 2015 (144)
3 SC_SNP ss15488563 Apr 01, 2015 (144)
4 SSAHASNP ss35183707 May 24, 2005 (125)
5 ABI ss40039718 Mar 13, 2006 (126)
6 HGSV ss78636057 Dec 07, 2007 (129)
7 BCMHGSC_JDW ss88443356 Mar 24, 2008 (129)
8 BGI ss106717865 Feb 05, 2009 (130)
9 ILLUMINA-UK ss118470249 Feb 14, 2009 (130)
10 ENSEMBL ss132255220 Dec 01, 2009 (131)
11 COMPLETE_GENOMICS ss170357132 Jul 04, 2010 (132)
12 BUSHMAN ss202334222 Jul 04, 2010 (132)
13 RSG_UW ss212961522 Jul 04, 2010 (132)
14 BL ss254846780 May 09, 2011 (134)
15 GMI ss280864831 May 04, 2012 (137)
16 PJP ss291104301 May 09, 2011 (134)
17 1000GENOMES ss336519677 May 09, 2011 (134)
18 TISHKOFF ss562354051 Apr 25, 2013 (138)
19 SSMP ss657706471 Apr 25, 2013 (138)
20 EVA-GONL ss988159260 Aug 21, 2014 (142)
21 1000GENOMES ss1339940370 Aug 21, 2014 (142)
22 DDI ss1426519299 Apr 01, 2015 (144)
23 EVA_GENOME_DK ss1575492376 Apr 01, 2015 (144)
24 EVA_MGP ss1711280492 Apr 01, 2015 (144)
25 HAMMER_LAB ss1806671575 Sep 08, 2015 (146)
26 WEILL_CORNELL_DGM ss1931523477 Feb 12, 2016 (147)
27 GENOMED ss1967278838 Jul 19, 2016 (147)
28 USC_VALOUEV ss2154788625 Dec 20, 2016 (150)
29 SYSTEMSBIOZJU ss2627719482 Nov 08, 2017 (151)
30 GRF ss2699058329 Nov 08, 2017 (151)
31 GNOMAD ss2895842114 Nov 08, 2017 (151)
32 SWEGEN ss3007523267 Nov 08, 2017 (151)
33 TOPMED ss3135966641 Nov 08, 2017 (151)
34 TOPMED ss3135966642 Nov 08, 2017 (151)
35 CSHL ss3349429961 Nov 08, 2017 (151)
36 OMUKHERJEE_ADBS ss3646421260 Oct 12, 2018 (152)
37 EVA_DECODE ss3691127420 Jul 13, 2019 (153)
38 ACPOP ss3737878958 Jul 13, 2019 (153)
39 EVA ss3748887237 Jul 13, 2019 (153)
40 PACBIO ss3786851788 Jul 13, 2019 (153)
41 PACBIO ss3792007054 Jul 13, 2019 (153)
42 PACBIO ss3796889071 Jul 13, 2019 (153)
43 KHV_HUMAN_GENOMES ss3814235632 Jul 13, 2019 (153)
44 EVA ss3839770465 Apr 26, 2020 (154)
45 EVA ss3845246447 Apr 26, 2020 (154)
46 SGDP_PRJ ss3875553127 Apr 26, 2020 (154)
47 KRGDB ss3923775937 Apr 26, 2020 (154)
48 KOGIC ss3969119499 Apr 26, 2020 (154)
49 FSA-LAB ss3983994708 Apr 26, 2021 (155)
50 EVA ss3986512468 Apr 26, 2021 (155)
51 TOPMED ss4873701620 Apr 26, 2021 (155)
52 TOMMO_GENOMICS ss5200490050 Apr 26, 2021 (155)
53 1000Genomes NC_000011.9 - 5269799 Oct 12, 2018 (152)
54 The Danish reference pan genome NC_000011.9 - 5269799 Apr 26, 2020 (154)
55 gnomAD - Genomes NC_000011.10 - 5248569 Apr 26, 2021 (155)
56 KOREAN population from KRGDB NC_000011.9 - 5269799 Apr 26, 2020 (154)
57 Korean Genome Project NC_000011.10 - 5248569 Apr 26, 2020 (154)
58 Medical Genome Project healthy controls from Spanish population NC_000011.9 - 5269799 Apr 26, 2020 (154)
59 Northern Sweden NC_000011.9 - 5269799 Jul 13, 2019 (153)
60 Qatari NC_000011.9 - 5269799 Apr 26, 2020 (154)
61 SGDP_PRJ NC_000011.9 - 5269799 Apr 26, 2020 (154)
62 Siberian NC_000011.9 - 5269799 Apr 26, 2020 (154)
63 8.3KJPN NC_000011.9 - 5269799 Apr 26, 2021 (155)
64 TopMed NC_000011.10 - 5248569 Apr 26, 2021 (155)
65 ALFA NC_000011.10 - 5248569 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).

Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
ss35183707, ss78636057, ss88443356, ss118470249, ss170357132, ss202334222, ss254846780, ss280864831, ss291104301 NC_000011.8:5226374:A:C NC_000011.10:5248568:A:C (self)
52416915, 2421790, 30953331, 396252, 11163823, 13565407, 27570107, 7304979, 58459357, ss336519677, ss562354051, ss657706471, ss988159260, ss1339940370, ss1426519299, ss1575492376, ss1711280492, ss1806671575, ss1931523477, ss1967278838, ss2154788625, ss2627719482, ss2699058329, ss2895842114, ss3007523267, ss3349429961, ss3646421260, ss3737878958, ss3748887237, ss3786851788, ss3792007054, ss3796889071, ss3839770465, ss3875553127, ss3923775937, ss3983994708, ss3986512468, ss5200490050 NC_000011.9:5269798:A:C NC_000011.10:5248568:A:C (self)
370119674, 25497500, 56041226, 89247276, 3957982414, ss3135966641, ss3691127420, ss3814235632, ss3845246447, ss3969119499, ss4873701620 NC_000011.10:5248568:A:C NC_000011.10:5248568:A:C (self)
ss15488563 NT_009237.16:4033738:A:C NC_000011.10:5248568:A:C (self)
ss40039718, ss106717865, ss132255220, ss212961522 NT_009237.18:5209798:A:C NC_000011.10:5248568:A:C (self)
ss11300756, ss12172269 NT_028310.10:4029971:A:C NC_000011.10:5248568:A:C (self)
3957982414, ss3135966642 NC_000011.10:5248568:A:T NC_000011.10:5248568:A:T (self)
Help

Publications tab displays PubMed articles citing the variation as a listing of PMID, Title, Author, Year, Journal, ordered by Year, descending.

4 citations for rs28440105
PMID Title Author Year Journal
18829352 High-density SNP genotyping to define beta-globin locus haplotypes. Liu L et al. 2009 Blood cells, molecules & diseases
27521862 Clinical, hematological and genetic data of a cohort of children with hemoglobin SD. Rezende Pdo V et al. 2016 Revista brasileira de hematologia e hemoterapia
28800727 A phased SNP-based classification of sickle cell anemia HBB haplotypes. Shaikho EM et al. 2017 BMC genomics
32448003 Prevalence and Diversity of Haplotypes of Sickle Cell Disease in the Eastern Province of Saudi Arabia. Al-Ali AK et al. 2020 Hemoglobin
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.post629+eb05767