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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.

rs191701880

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr6:3406625 (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
G>T
Variation Type
SNV Single Nucleotide Variation
Frequency
T=0.001647 (436/264690, TOPMED)
T=0.001599 (224/140062, GnomAD)
T=0.00159 (30/18890, ALFA) (+ 9 more)
T=0.0011 (7/6404, 1000G_30x)
T=0.0010 (5/5008, 1000G)
T=0.0007 (3/4480, Estonian)
T=0.0031 (12/3854, ALSPAC)
T=0.0032 (12/3708, TWINSUK)
T=0.007 (4/600, NorthernSweden)
T=0.005 (1/216, Qatari)
G=0.5 (1/2, SGDP_PRJ)
T=0.5 (1/2, SGDP_PRJ)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
SLC22A23 : 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 18890 G=0.99841 T=0.00159
European Sub 14286 G=0.99804 T=0.00196
African Sub 2946 G=0.9997 T=0.0003
African Others Sub 114 G=1.000 T=0.000
African American Sub 2832 G=0.9996 T=0.0004
Asian Sub 112 G=1.000 T=0.000
East Asian Sub 86 G=1.00 T=0.00
Other Asian Sub 26 G=1.00 T=0.00
Latin American 1 Sub 146 G=1.000 T=0.000
Latin American 2 Sub 610 G=1.000 T=0.000
South Asian Sub 98 G=1.00 T=0.00
Other Sub 692 G=0.999 T=0.001


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 G=0.998353 T=0.001647
gnomAD - Genomes Global Study-wide 140062 G=0.998401 T=0.001599
gnomAD - Genomes European Sub 75896 G=0.99800 T=0.00200
gnomAD - Genomes African Sub 41946 G=0.99924 T=0.00076
gnomAD - Genomes American Sub 13620 G=0.99794 T=0.00206
gnomAD - Genomes Ashkenazi Jewish Sub 3320 G=0.9967 T=0.0033
gnomAD - Genomes East Asian Sub 3130 G=1.0000 T=0.0000
gnomAD - Genomes Other Sub 2150 G=0.9995 T=0.0005
Allele Frequency Aggregator Total Global 18890 G=0.99841 T=0.00159
Allele Frequency Aggregator European Sub 14286 G=0.99804 T=0.00196
Allele Frequency Aggregator African Sub 2946 G=0.9997 T=0.0003
Allele Frequency Aggregator Other Sub 692 G=0.999 T=0.001
Allele Frequency Aggregator Latin American 2 Sub 610 G=1.000 T=0.000
Allele Frequency Aggregator Latin American 1 Sub 146 G=1.000 T=0.000
Allele Frequency Aggregator Asian Sub 112 G=1.000 T=0.000
Allele Frequency Aggregator South Asian Sub 98 G=1.00 T=0.00
1000Genomes_30x Global Study-wide 6404 G=0.9989 T=0.0011
1000Genomes_30x African Sub 1786 G=1.0000 T=0.0000
1000Genomes_30x Europe Sub 1266 G=0.9984 T=0.0016
1000Genomes_30x South Asian Sub 1202 G=1.0000 T=0.0000
1000Genomes_30x East Asian Sub 1170 G=1.0000 T=0.0000
1000Genomes_30x American Sub 980 G=0.995 T=0.005
1000Genomes Global Study-wide 5008 G=0.9990 T=0.0010
1000Genomes African Sub 1322 G=1.0000 T=0.0000
1000Genomes East Asian Sub 1008 G=1.0000 T=0.0000
1000Genomes Europe Sub 1006 G=0.9980 T=0.0020
1000Genomes South Asian Sub 978 G=1.000 T=0.000
1000Genomes American Sub 694 G=0.996 T=0.004
Genetic variation in the Estonian population Estonian Study-wide 4480 G=0.9993 T=0.0007
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 G=0.9969 T=0.0031
UK 10K study - Twins TWIN COHORT Study-wide 3708 G=0.9968 T=0.0032
Northern Sweden ACPOP Study-wide 600 G=0.993 T=0.007
Qatari Global Study-wide 216 G=0.995 T=0.005
SGDP_PRJ Global Study-wide 2 G=0.5 T=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 6 NC_000006.12:g.3406625G>T
GRCh37.p13 chr 6 NC_000006.11:g.3406859G>T
Gene: SLC22A23, solute carrier family 22 member 23 (minus strand)
Molecule type Change Amino acid[Codon] SO Term
SLC22A23 transcript variant 3 NM_001286455.1:c.70+3563C…

NM_001286455.1:c.70+3563C>A

N/A Intron Variant
SLC22A23 transcript variant 4 NM_001286456.2:c.913+3563…

NM_001286456.2:c.913+3563C>A

N/A Intron Variant
SLC22A23 transcript variant 6 NM_001382317.1:c.913+3563…

NM_001382317.1:c.913+3563C>A

N/A Intron Variant
SLC22A23 transcript variant 9 NM_001382320.1:c.654+4928…

NM_001382320.1:c.654+49281C>A

N/A Intron Variant
SLC22A23 transcript variant 1 NM_015482.2:c.913+3563C>A N/A Intron Variant
SLC22A23 transcript variant 2 NM_021945.6:c.70+3563C>A N/A Intron Variant
SLC22A23 transcript variant 7 NM_001382318.1:c. N/A Genic Upstream Transcript Variant
SLC22A23 transcript variant 8 NM_001382319.1:c. N/A Genic Upstream Transcript Variant
SLC22A23 transcript variant 10 NM_001382321.1:c. N/A Genic Upstream Transcript Variant
SLC22A23 transcript variant 5 NR_104448.1:n. N/A Intron Variant
SLC22A23 transcript variant 11 NR_168069.1:n. N/A Intron Variant
SLC22A23 transcript variant X1 XM_011514801.3:c.985+3563…

XM_011514801.3:c.985+3563C>A

N/A Intron Variant
SLC22A23 transcript variant X5 XM_017011180.2:c.391+3563…

XM_017011180.2:c.391+3563C>A

N/A Intron Variant
SLC22A23 transcript variant X3 XM_017011183.2:c.985+3563…

XM_017011183.2:c.985+3563C>A

N/A Intron Variant
SLC22A23 transcript variant X4 XM_017011185.3:c.985+3563…

XM_017011185.3:c.985+3563C>A

N/A Intron Variant
SLC22A23 transcript variant X11 XM_017011186.2:c.70+3563C…

XM_017011186.2:c.70+3563C>A

N/A Intron Variant
SLC22A23 transcript variant X9 XM_047419243.1:c.-4319= N/A 5 Prime UTR Variant
SLC22A23 transcript variant X7 XM_017011184.2:c. N/A Genic Upstream Transcript Variant
SLC22A23 transcript variant X6 XM_047419241.1:c. N/A Genic Upstream Transcript Variant
SLC22A23 transcript variant X8 XM_047419242.1:c. N/A Genic Upstream Transcript Variant
SLC22A23 transcript variant X12 XM_047419244.1:c. N/A Genic Downstream Transcript Variant
SLC22A23 transcript variant X2 XR_001743575.2:n. N/A Intron Variant
SLC22A23 transcript variant X10 XR_007059328.1:n. 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 G= T
GRCh38.p14 chr 6 NC_000006.12:g.3406625= NC_000006.12:g.3406625G>T
GRCh37.p13 chr 6 NC_000006.11:g.3406859= NC_000006.11:g.3406859G>T
SLC22A23 transcript variant X9 XM_047419243.1:c.-4319= XM_047419243.1:c.-4319C>A
SLC22A23 transcript variant 3 NM_001286455.1:c.70+3563= NM_001286455.1:c.70+3563C>A
SLC22A23 transcript variant 4 NM_001286456.2:c.913+3563= NM_001286456.2:c.913+3563C>A
SLC22A23 transcript variant 6 NM_001382317.1:c.913+3563= NM_001382317.1:c.913+3563C>A
SLC22A23 transcript variant 9 NM_001382320.1:c.654+49281= NM_001382320.1:c.654+49281C>A
SLC22A23 transcript variant 1 NM_015482.1:c.913+3563= NM_015482.1:c.913+3563C>A
SLC22A23 transcript variant 1 NM_015482.2:c.913+3563= NM_015482.2:c.913+3563C>A
SLC22A23 transcript variant 2 NM_021945.5:c.70+3563= NM_021945.5:c.70+3563C>A
SLC22A23 transcript variant 2 NM_021945.6:c.70+3563= NM_021945.6:c.70+3563C>A
SLC22A23 transcript variant X1 XM_005249285.1:c.913+3563= XM_005249285.1:c.913+3563C>A
SLC22A23 transcript variant X2 XM_005249286.1:c.70+3563= XM_005249286.1:c.70+3563C>A
SLC22A23 transcript variant X1 XM_011514801.3:c.985+3563= XM_011514801.3:c.985+3563C>A
SLC22A23 transcript variant X5 XM_017011180.2:c.391+3563= XM_017011180.2:c.391+3563C>A
SLC22A23 transcript variant X3 XM_017011183.2:c.985+3563= XM_017011183.2:c.985+3563C>A
SLC22A23 transcript variant X4 XM_017011185.3:c.985+3563= XM_017011185.3:c.985+3563C>A
SLC22A23 transcript variant X11 XM_017011186.2:c.70+3563= XM_017011186.2:c.70+3563C>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#.

19 SubSNP, 11 Frequency submissions
No Submitter Submission ID Date (Build)
1 1000GENOMES ss458633485 Sep 17, 2011 (135)
2 1000GENOMES ss1318732972 Aug 21, 2014 (142)
3 EVA_UK10K_ALSPAC ss1614819174 Apr 01, 2015 (144)
4 EVA_UK10K_TWINSUK ss1657813207 Apr 01, 2015 (144)
5 WEILL_CORNELL_DGM ss1925777723 Feb 12, 2016 (147)
6 HUMAN_LONGEVITY ss2281300780 Dec 20, 2016 (150)
7 GNOMAD ss2835128421 Nov 08, 2017 (151)
8 SWEGEN ss2998418075 Nov 08, 2017 (151)
9 EGCUT_WGS ss3666341664 Jul 13, 2019 (153)
10 ACPOP ss3733148768 Jul 13, 2019 (153)
11 SGDP_PRJ ss3863791646 Apr 26, 2020 (154)
12 TOPMED ss4691689579 Apr 26, 2021 (155)
13 1000G_HIGH_COVERAGE ss5267189256 Oct 13, 2022 (156)
14 EVA ss5363426176 Oct 13, 2022 (156)
15 HUGCELL_USP ss5465002559 Oct 13, 2022 (156)
16 1000G_HIGH_COVERAGE ss5552515885 Oct 13, 2022 (156)
17 EVA ss5841709214 Oct 13, 2022 (156)
18 EVA ss5882410907 Oct 13, 2022 (156)
19 EVA ss5968138705 Oct 13, 2022 (156)
20 1000Genomes NC_000006.11 - 3406859 Oct 12, 2018 (152)
21 1000Genomes_30x NC_000006.12 - 3406625 Oct 13, 2022 (156)
22 The Avon Longitudinal Study of Parents and Children NC_000006.11 - 3406859 Oct 12, 2018 (152)
23 Genetic variation in the Estonian population NC_000006.11 - 3406859 Oct 12, 2018 (152)
24 gnomAD - Genomes NC_000006.12 - 3406625 Apr 26, 2021 (155)
25 Northern Sweden NC_000006.11 - 3406859 Jul 13, 2019 (153)
26 Qatari NC_000006.11 - 3406859 Apr 26, 2020 (154)
27 SGDP_PRJ NC_000006.11 - 3406859 Apr 26, 2020 (154)
28 TopMed NC_000006.12 - 3406625 Apr 26, 2021 (155)
29 UK 10K study - Twins NC_000006.11 - 3406859 Oct 12, 2018 (152)
30 ALFA NC_000006.12 - 3406625 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
30466000, 16957201, 12079912, 6433633, 7819653, 15808626, 16957201, ss458633485, ss1318732972, ss1614819174, ss1657813207, ss1925777723, ss2835128421, ss2998418075, ss3666341664, ss3733148768, ss3863791646, ss5363426176, ss5841709214, ss5968138705 NC_000006.11:3406858:G:T NC_000006.12:3406624:G:T (self)
40041820, 215419997, 529067137, 5648741179, ss2281300780, ss4691689579, ss5267189256, ss5465002559, ss5552515885, ss5882410907 NC_000006.12:3406624:G:T NC_000006.12:3406624:G:T (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 rs191701880

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