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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.

rs28406733

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chrY:12163 (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.

This SNP has mapping conflicts. See here for details.

Alleles
G>A / G>C
Variation Type
SNV Single Nucleotide Variation
Frequency
A=0.27074 (4530/16732, 8.3KJPN)
A=0.19465 (3179/16332, ALFA)
A=0.00058 (9/15636, 14KJPN) (+ 7 more)
A=0.4776 (1803/3775, 1000G)
A=0.002 (1/534, MGP)
G=0.306 (104/340, SGDP_PRJ)
A=0.481 (52/108, Qatari)
G=0.45 (18/40, GENOME_DK)
A=0.22 (7/32, Vietnamese)
G=0.0 (0/2, KOREAN)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
None
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 16332 G=0.80535 A=0.19465
European Sub 12080 G=0.78245 A=0.21755
African Sub 2816 G=0.8114 A=0.1886
African Others Sub 108 G=0.731 A=0.269
African American Sub 2708 G=0.8146 A=0.1854
Asian Sub 108 G=1.000 A=0.000
East Asian Sub 84 G=1.00 A=0.00
Other Asian Sub 24 G=1.00 A=0.00
Latin American 1 Sub 146 G=0.979 A=0.021
Latin American 2 Sub 610 G=1.000 A=0.000
South Asian Sub 94 G=1.00 A=0.00
Other Sub 478 G=0.964 A=0.036


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
8.3KJPN JAPANESE Study-wide 16732 G=0.72926 A=0.27074
Allele Frequency Aggregator Total Global 16332 G=0.80535 A=0.19465
Allele Frequency Aggregator European Sub 12080 G=0.78245 A=0.21755
Allele Frequency Aggregator African Sub 2816 G=0.8114 A=0.1886
Allele Frequency Aggregator Latin American 2 Sub 610 G=1.000 A=0.000
Allele Frequency Aggregator Other Sub 478 G=0.964 A=0.036
Allele Frequency Aggregator Latin American 1 Sub 146 G=0.979 A=0.021
Allele Frequency Aggregator Asian Sub 108 G=1.000 A=0.000
Allele Frequency Aggregator South Asian Sub 94 G=1.00 A=0.00
14KJPN JAPANESE Study-wide 15636 G=0.99942 A=0.00058
1000Genomes Global Study-wide 3775 G=0.5224 A=0.4776
1000Genomes African Sub 1003 G=0.2971 A=0.7029
1000Genomes Europe Sub 766 G=0.493 A=0.507
1000Genomes East Asian Sub 764 G=0.688 A=0.312
1000Genomes South Asian Sub 718 G=0.632 A=0.368
1000Genomes American Sub 524 G=0.603 A=0.397
Medical Genome Project healthy controls from Spanish population Spanish controls Study-wide 534 G=0.998 A=0.002
SGDP_PRJ Global Study-wide 340 G=0.306 A=0.694
Qatari Global Study-wide 108 G=0.519 A=0.481
The Danish reference pan genome Danish Study-wide 40 G=0.45 A=0.55
A Vietnamese Genetic Variation Database Global Study-wide 32 G=0.78 A=0.22
KOREAN population from KRGDB KOREAN Study-wide 2 G=0.0 A=1.0
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 Y NC_000024.10:g.12163G>A
GRCh38.p14 chr Y NC_000024.10:g.12163G>C
GRCh37.p13 chr Y NC_000024.9:g.12163G>A
GRCh37.p13 chr Y NC_000024.9:g.12163G>C
GRCh38.p14 chr X NC_000023.11:g.12163G>A
GRCh38.p14 chr X NC_000023.11:g.12163G>C
GRCh37.p13 chr X NC_000023.10:g.62163G>A
GRCh37.p13 chr X NC_000023.10:g.62163G>C
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 C
GRCh38.p14 chr Y NC_000024.10:g.12163= NC_000024.10:g.12163G>A NC_000024.10:g.12163G>C
GRCh37.p13 chr Y NC_000024.9:g.12163= NC_000024.9:g.12163G>A NC_000024.9:g.12163G>C
GRCh38.p14 chr X NC_000023.11:g.12163= NC_000023.11:g.12163G>A NC_000023.11:g.12163G>C
GRCh37.p13 chr X NC_000023.10:g.62163= NC_000023.10:g.62163G>A NC_000023.10:g.62163G>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#.

31 SubSNP, 10 Frequency submissions
No Submitter Submission ID Date (Build)
1 SSAHASNP ss35113067 May 24, 2005 (125)
2 HGSV ss83373150 Dec 16, 2007 (130)
3 1000GENOMES ss112735567 Feb 05, 2009 (131)
4 ILLUMINA-UK ss115582605 Feb 14, 2009 (131)
5 ENSEMBL ss144452737 Sep 28, 2016 (149)
6 COMPLETE_GENOMICS ss162979559 Jul 04, 2010 (132)
7 COMPLETE_GENOMICS ss164236131 Jul 04, 2010 (132)
8 COMPLETE_GENOMICS ss165986713 Jul 04, 2010 (132)
9 1000GENOMES ss212139071 Jul 15, 2010 (132)
10 1000GENOMES ss341248344 May 09, 2011 (137)
11 SSMP ss662653140 Apr 25, 2013 (138)
12 1000GENOMES ss1553226394 Apr 01, 2015 (144)
13 EVA_GENOME_DK ss1583300946 Apr 01, 2015 (144)
14 EVA_MGP ss1711575574 Apr 01, 2015 (144)
15 WEILL_CORNELL_DGM ss1939051236 Feb 12, 2016 (147)
16 GENOMED ss1971330013 Jul 19, 2016 (147)
17 SYSTEMSBIOZJU ss2629645747 Nov 08, 2017 (151)
18 GNOMAD ss2975740032 Nov 08, 2017 (151)
19 SWEGEN ss3019504001 Nov 08, 2017 (151)
20 EVA ss3769834827 Jul 14, 2019 (153)
21 PACBIO ss3788859125 Jul 14, 2019 (153)
22 PACBIO ss3793720490 Jul 14, 2019 (153)
23 PACBIO ss3798607010 Jul 14, 2019 (153)
24 KHV_HUMAN_GENOMES ss3822692011 Jul 14, 2019 (153)
25 EVA ss3836054662 Apr 27, 2020 (154)
26 SGDP_PRJ ss3890816545 Apr 27, 2020 (154)
27 KRGDB ss3941223415 Apr 27, 2020 (154)
28 TOMMO_GENOMICS ss5233200241 Apr 27, 2021 (155)
29 SANFORD_IMAGENETICS ss5664735602 Oct 13, 2022 (156)
30 TOMMO_GENOMICS ss5794509308 Oct 13, 2022 (156)
31 EVA ss5977701047 Oct 13, 2022 (156)
32 1000Genomes NC_000023.10 - 62163 Oct 13, 2018 (152)
33 The Danish reference pan genome NC_000023.10 - 62163 Apr 27, 2020 (154)
34 KOREAN population from KRGDB NC_000023.10 - 62163 Apr 27, 2020 (154)
35 Medical Genome Project healthy controls from Spanish population NC_000023.10 - 62163 Apr 27, 2020 (154)
36 Qatari NC_000023.10 - 62163 Apr 27, 2020 (154)
37 SGDP_PRJ NC_000023.10 - 62163 Apr 27, 2020 (154)
38 8.3KJPN NC_000023.10 - 62163 Apr 27, 2021 (155)
39 14KJPN NC_000023.11 - 12163 Oct 13, 2022 (156)
40 A Vietnamese Genetic Variation Database NC_000023.10 - 62163 Jul 14, 2019 (153)
41 ALFA NC_000024.10 - 12163 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)
rs61344611 May 26, 2008 (130)
rs67575831 Dec 02, 2009 (131)
rs144676859 May 04, 2012 (137)
Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
ss35113067, ss83373150 NC_000023.8:2162:G:A NC_000024.10:12162:G:A (self)
ss112735567, ss115582605, ss162979559, ss164236131, ss165986713, ss212139071 NC_000023.9:2162:G:A NC_000024.10:12162:G:A (self)
81214330, 9465883, 48400809, 691334, 21093158, 42833525, 91169548, 9906001, ss341248344, ss662653140, ss1553226394, ss1583300946, ss1711575574, ss1939051236, ss1971330013, ss2629645747, ss2975740032, ss3019504001, ss3769834827, ss3788859125, ss3793720490, ss3798607010, ss3836054662, ss3890816545, ss3941223415, ss5233200241, ss5664735602, ss5977701047 NC_000023.10:62162:G:A NC_000024.10:12162:G:A (self)
128346412, ss3822692011, ss5794509308 NC_000023.11:12162:G:A NC_000024.10:12162:G:A (self)
14183097564 NC_000024.10:12162:G:A NC_000024.10:12162:G:A (self)
ss144452737 NT_167199.1:2162:G:A NC_000024.10:12162:G:A (self)
ss2975740032 NC_000023.10:62162:G:C NC_000024.10:12162:G: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 rs28406733

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