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dbSNP Short Genetic Variations

Examples: rs268, BRCA1 and more Advanced search

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.

rs11568388

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr9:84290204 (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
C>T
Variation Type
SNV Single Nucleotide Variation
Frequency
T=0.000008 (2/264690, TOPMED)
T=0.00000 (0/30388, ALFA)
T=0.00004 (1/28258, 14KJPN) (+ 5 more)
T=0.00006 (1/16760, 8.3KJPN)
T=0.0003 (1/3854, ALSPAC)
T=0.0000 (0/3708, TWINSUK)
T=0.002 (1/550, PharmGKB)
T=0.000 (0/330, HapMap)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
SLC28A3 : Missense Variant
LOC105376116 : 500B Downstream Variant
Publications
2 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 30388 C=1.00000 T=0.00000
European Sub 25756 C=1.00000 T=0.00000
African Sub 2898 C=1.0000 T=0.0000
African Others Sub 114 C=1.000 T=0.000
African American Sub 2784 C=1.0000 T=0.0000
Asian Sub 156 C=1.000 T=0.000
East Asian Sub 130 C=1.000 T=0.000
Other Asian Sub 26 C=1.00 T=0.00
Latin American 1 Sub 146 C=1.000 T=0.000
Latin American 2 Sub 610 C=1.000 T=0.000
South Asian Sub 98 C=1.00 T=0.00
Other Sub 724 C=1.000 T=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 C=0.999992 T=0.000008
Allele Frequency Aggregator Total Global 30388 C=1.00000 T=0.00000
Allele Frequency Aggregator European Sub 25756 C=1.00000 T=0.00000
Allele Frequency Aggregator African Sub 2898 C=1.0000 T=0.0000
Allele Frequency Aggregator Other Sub 724 C=1.000 T=0.000
Allele Frequency Aggregator Latin American 2 Sub 610 C=1.000 T=0.000
Allele Frequency Aggregator Asian Sub 156 C=1.000 T=0.000
Allele Frequency Aggregator Latin American 1 Sub 146 C=1.000 T=0.000
Allele Frequency Aggregator South Asian Sub 98 C=1.00 T=0.00
14KJPN JAPANESE Study-wide 28258 C=0.99996 T=0.00004
8.3KJPN JAPANESE Study-wide 16760 C=0.99994 T=0.00006
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 C=0.9997 T=0.0003
UK 10K study - Twins TWIN COHORT Study-wide 3708 C=1.0000 T=0.0000
PharmGKB Aggregated Global Study-wide 550 C=0.998 T=0.002
PharmGKB Aggregated PA129462072 Sub 550 C=0.998 T=0.002
HapMap Global Study-wide 330 C=1.000 T=0.000
HapMap African Sub 120 C=1.000 T=0.000
HapMap American Sub 120 C=1.000 T=0.000
HapMap Asian Sub 90 C=1.00 T=0.00
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 9 NC_000009.12:g.84290204C>T
GRCh37.p13 chr 9 NC_000009.11:g.86905119C>T
Gene: SLC28A3, solute carrier family 28 member 3 (minus strand)
Molecule type Change Amino acid[Codon] SO Term
SLC28A3 transcript variant 1 NM_001199633.2:c.1099G>A G [GGG] > R [AGG] Coding Sequence Variant
solute carrier family 28 member 3 NP_001186562.1:p.Gly367Arg G (Gly) > R (Arg) Missense Variant
SLC28A3 transcript variant 2 NM_022127.3:c.1099G>A G [GGG] > R [AGG] Coding Sequence Variant
solute carrier family 28 member 3 NP_071410.1:p.Gly367Arg G (Gly) > R (Arg) Missense Variant
SLC28A3 transcript variant 3 NR_037638.3:n.1400G>A N/A Non Coding Transcript Variant
SLC28A3 transcript variant X7 XM_011518910.3:c.*116= N/A 3 Prime UTR Variant
SLC28A3 transcript variant X6 XM_011518909.3:c. N/A Genic Downstream Transcript Variant
SLC28A3 transcript variant X1 XM_011518905.3:c.1183G>A G [GGG] > R [AGG] Coding Sequence Variant
solute carrier family 28 member 3 isoform X1 XP_011517207.1:p.Gly395Arg G (Gly) > R (Arg) Missense Variant
SLC28A3 transcript variant X2 XM_011518906.3:c.1183G>A G [GGG] > R [AGG] Coding Sequence Variant
solute carrier family 28 member 3 isoform X1 XP_011517208.1:p.Gly395Arg G (Gly) > R (Arg) Missense Variant
SLC28A3 transcript variant X3 XM_011518907.3:c.850G>A G [GGG] > R [AGG] Coding Sequence Variant
solute carrier family 28 member 3 isoform X2 XP_011517209.1:p.Gly284Arg G (Gly) > R (Arg) Missense Variant
SLC28A3 transcript variant X4 XM_047423712.1:c.1183G>A G [GGG] > R [AGG] Coding Sequence Variant
solute carrier family 28 member 3 isoform X3 XP_047279668.1:p.Gly395Arg G (Gly) > R (Arg) Missense Variant
SLC28A3 transcript variant X5 XM_011518908.3:c.460G>A G [GGG] > R [AGG] Coding Sequence Variant
solute carrier family 28 member 3 isoform X4 XP_011517210.1:p.Gly154Arg G (Gly) > R (Arg) Missense Variant
Gene: LOC105376116, uncharacterized LOC105376116 (plus strand) : 500B Downstream Variant
Molecule type Change Amino acid[Codon] SO Term
SLC28A3-AS1 transcript XR_001746802.1:n. N/A Downstream Transcript 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 C= T
GRCh38.p14 chr 9 NC_000009.12:g.84290204= NC_000009.12:g.84290204C>T
GRCh37.p13 chr 9 NC_000009.11:g.86905119= NC_000009.11:g.86905119C>T
SLC28A3 transcript variant X2 XM_011518906.3:c.1183= XM_011518906.3:c.1183G>A
SLC28A3 transcript variant X2 XM_011518906.2:c.1183= XM_011518906.2:c.1183G>A
SLC28A3 transcript variant X2 XM_011518906.1:c.1183= XM_011518906.1:c.1183G>A
SLC28A3 transcript variant 2 NM_022127.3:c.1099= NM_022127.3:c.1099G>A
SLC28A3 transcript variant 2 NM_022127.2:c.1099= NM_022127.2:c.1099G>A
SLC28A3 transcript variant 3 NR_037638.3:n.1400= NR_037638.3:n.1400G>A
SLC28A3 transcript variant 3 NR_037638.2:n.1421= NR_037638.2:n.1421G>A
SLC28A3 transcript variant X1 XM_011518905.3:c.1183= XM_011518905.3:c.1183G>A
SLC28A3 transcript variant X1 XM_011518905.2:c.1183= XM_011518905.2:c.1183G>A
SLC28A3 transcript variant X1 XM_011518905.1:c.1183= XM_011518905.1:c.1183G>A
SLC28A3 transcript variant X3 XM_011518907.3:c.850= XM_011518907.3:c.850G>A
SLC28A3 transcript variant X3 XM_011518907.2:c.850= XM_011518907.2:c.850G>A
SLC28A3 transcript variant X3 XM_011518907.1:c.850= XM_011518907.1:c.850G>A
SLC28A3 transcript variant X5 XM_011518908.3:c.460= XM_011518908.3:c.460G>A
SLC28A3 transcript variant X5 XM_011518908.2:c.460= XM_011518908.2:c.460G>A
SLC28A3 transcript variant X5 XM_011518908.1:c.460= XM_011518908.1:c.460G>A
SLC28A3 transcript variant X7 XM_011518910.3:c.*116= XM_011518910.3:c.*116G>A
SLC28A3 transcript variant X7 XM_011518910.2:c.*116= XM_011518910.2:c.*116G>A
SLC28A3 transcript variant X7 XM_011518910.1:c.*116= XM_011518910.1:c.*116G>A
SLC28A3 transcript variant 1 NM_001199633.2:c.1099= NM_001199633.2:c.1099G>A
SLC28A3 transcript variant 1 NM_001199633.1:c.1099= NM_001199633.1:c.1099G>A
SLC28A3 transcript variant X4 XM_047423712.1:c.1183= XM_047423712.1:c.1183G>A
solute carrier family 28 member 3 isoform X1 XP_011517208.1:p.Gly395= XP_011517208.1:p.Gly395Arg
solute carrier family 28 member 3 NP_071410.1:p.Gly367= NP_071410.1:p.Gly367Arg
solute carrier family 28 member 3 isoform X1 XP_011517207.1:p.Gly395= XP_011517207.1:p.Gly395Arg
solute carrier family 28 member 3 isoform X2 XP_011517209.1:p.Gly284= XP_011517209.1:p.Gly284Arg
solute carrier family 28 member 3 isoform X4 XP_011517210.1:p.Gly154= XP_011517210.1:p.Gly154Arg
solute carrier family 28 member 3 NP_001186562.1:p.Gly367= NP_001186562.1:p.Gly367Arg
solute carrier family 28 member 3 isoform X3 XP_047279668.1:p.Gly395= XP_047279668.1:p.Gly395Arg
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#.

7 SubSNP, 8 Frequency submissions
No Submitter Submission ID Date (Build)
1 PHARMGKB_PMT ss69370466 May 18, 2007 (127)
2 EVA_UK10K_ALSPAC ss1622966318 Apr 01, 2015 (144)
3 EVA_UK10K_TWINSUK ss1665960351 Apr 01, 2015 (144)
4 ILLUMINA ss2711165292 Nov 08, 2017 (151)
5 TOPMED ss4825854209 Apr 26, 2021 (155)
6 TOMMO_GENOMICS ss5194035508 Apr 26, 2021 (155)
7 TOMMO_GENOMICS ss5738187703 Oct 13, 2022 (156)
8 The Avon Longitudinal Study of Parents and Children NC_000009.11 - 86905119 Oct 12, 2018 (152)
9 HapMap NC_000009.12 - 84290204 Apr 26, 2020 (154)
10 PharmGKB Aggregated NC_000009.12 - 84290204 Apr 26, 2020 (154)
11 8.3KJPN NC_000009.11 - 86905119 Apr 26, 2021 (155)
12 14KJPN NC_000009.12 - 84290204 Oct 13, 2022 (156)
13 TopMed NC_000009.12 - 84290204 Apr 26, 2021 (155)
14 UK 10K study - Twins NC_000009.11 - 86905119 Oct 12, 2018 (152)
15 ALFA NC_000009.12 - 84290204 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).

Associated ID History Updated (Build)
rs45599235 Mar 05, 2008 (129)
Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
25892926, 52004815, 25892926, ss1622966318, ss1665960351, ss2711165292, ss5194035508 NC_000009.11:86905118:C:T NC_000009.12:84290203:C:T (self)
3856311, 12663, 72024807, 663231770, 11189282787, ss4825854209, ss5738187703 NC_000009.12:84290203:C:T NC_000009.12:84290203:C:T (self)
ss69370466 NT_008470.19:16069650:C:T NC_000009.12:84290203:C:T (self)
Help

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

2 citations for rs11568388
PMID Title Author Year Journal
19940846 The pharmacogenomics of membrane transporters project: research at the interface of genomics and transporter pharmacology. Kroetz DL et al. 2010 Clinical pharmacology and therapeutics
24944790 Screening for 392 polymorphisms in 141 pharmacogenes. Kim JY et al. 2014 Biomedical reports
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