Name: rs74671366
Published: September 21, 2022
License: Open Access

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.

rs74671366

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr6:3288082 (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>A
Variation Type: SNV Single Nucleotide Variation
Frequency: A=0.010117 (2678/264690, TOPMED)
A=0.010614 (1488/140194, GnomAD)
A=0.00522 (184/35248, ALFA) (+ 12 more)
A=0.00004 (1/28258, 14KJPN)
A=0.00006 (1/16760, 8.3KJPN)
A=0.0109 (70/6404, 1000G_30x)
A=0.0096 (48/5008, 1000G)
A=0.0004 (2/4480, Estonian)
A=0.0078 (30/3854, ALSPAC)
A=0.0062 (23/3708, TWINSUK)
A=0.002 (2/998, GoNL)
G=0.5 (2/4, SGDP_PRJ)
A=0.5 (2/4, SGDP_PRJ)
G=0.5 (1/2, Siberian)
A=0.5 (1/2, Siberian)

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	35248	G=0.99478	A=0.00522
European	Sub	30372	G=0.99605	A=0.00395
African	Sub	2946	G=0.9813	A=0.0187
African Others	Sub	114	G=0.974	A=0.026
African American	Sub	2832	G=0.9816	A=0.0184
Asian	Sub	156	G=1.000	A=0.000
East Asian	Sub	130	G=1.000	A=0.000
Other Asian	Sub	26	G=1.00	A=0.00
Latin American 1	Sub	146	G=1.000	A=0.000
Latin American 2	Sub	610	G=0.995	A=0.005
South Asian	Sub	98	G=1.00	A=0.00
Other	Sub	920	G=0.993	A=0.007

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").

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Study	Population	Group	Sample Size	Ref Allele	Alt Allele
TopMed	Global	Study-wide	264690	G=0.989883	A=0.010117
gnomAD - Genomes	Global	Study-wide	140194	G=0.989386	A=0.010614
gnomAD - Genomes	European	Sub	75938	G=0.99486	A=0.00514
gnomAD - Genomes	African	Sub	41998	G=0.97614	A=0.02386
gnomAD - Genomes	American	Sub	13648	G=0.99487	A=0.00513
gnomAD - Genomes	Ashkenazi Jewish	Sub	3324	G=0.9958	A=0.0042
gnomAD - Genomes	East Asian	Sub	3134	G=0.9997	A=0.0003
gnomAD - Genomes	Other	Sub	2152	G=0.9949	A=0.0051
Allele Frequency Aggregator	Total	Global	35248	G=0.99478	A=0.00522
Allele Frequency Aggregator	European	Sub	30372	G=0.99605	A=0.00395
Allele Frequency Aggregator	African	Sub	2946	G=0.9813	A=0.0187
Allele Frequency Aggregator	Other	Sub	920	G=0.993	A=0.007
Allele Frequency Aggregator	Latin American 2	Sub	610	G=0.995	A=0.005
Allele Frequency Aggregator	Asian	Sub	156	G=1.000	A=0.000
Allele Frequency Aggregator	Latin American 1	Sub	146	G=1.000	A=0.000
Allele Frequency Aggregator	South Asian	Sub	98	G=1.00	A=0.00
14KJPN	JAPANESE	Study-wide	28258	G=0.99996	A=0.00004
8.3KJPN	JAPANESE	Study-wide	16760	G=0.99994	A=0.00006
1000Genomes_30x	Global	Study-wide	6404	G=0.9891	A=0.0109
1000Genomes_30x	African	Sub	1786	G=0.9681	A=0.0319
1000Genomes_30x	Europe	Sub	1266	G=0.9953	A=0.0047
1000Genomes_30x	South Asian	Sub	1202	G=1.0000	A=0.0000
1000Genomes_30x	East Asian	Sub	1170	G=1.0000	A=0.0000
1000Genomes_30x	American	Sub	980	G=0.993	A=0.007
1000Genomes	Global	Study-wide	5008	G=0.9904	A=0.0096
1000Genomes	African	Sub	1322	G=0.9682	A=0.0318
1000Genomes	East Asian	Sub	1008	G=1.0000	A=0.0000
1000Genomes	Europe	Sub	1006	G=0.9990	A=0.0010
1000Genomes	South Asian	Sub	978	G=1.000	A=0.000
1000Genomes	American	Sub	694	G=0.993	A=0.007
Genetic variation in the Estonian population	Estonian	Study-wide	4480	G=0.9996	A=0.0004
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	G=0.9922	A=0.0078
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	G=0.9938	A=0.0062
Genome of the Netherlands Release 5	Genome of the Netherlands	Study-wide	998	G=0.998	A=0.002
SGDP_PRJ	Global	Study-wide	4	G=0.5	A=0.5
Siberian	Global	Study-wide	2	G=0.5	A=0.5

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.3288082G>A
GRCh37.p13 chr 6	NC_000006.11:g.3288316G>A

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.471-991C… NM_001286455.1:c.471-991C>T	N/A	Intron Variant
SLC22A23 transcript variant 6	NM_001382317.1:c.1314-991… NM_001382317.1:c.1314-991C>T	N/A	Intron Variant
SLC22A23 transcript variant 7	NM_001382318.1:c.423-991C… NM_001382318.1:c.423-991C>T	N/A	Intron Variant
SLC22A23 transcript variant 8	NM_001382319.1:c.423-991C… NM_001382319.1:c.423-991C>T	N/A	Intron Variant
SLC22A23 transcript variant 1	NM_015482.2:c.1314-991C>T	N/A	Intron Variant
SLC22A23 transcript variant 2	NM_021945.6:c.471-991C>T	N/A	Intron Variant
SLC22A23 transcript variant 4	NM_001286456.2:c.	N/A	Genic Downstream Transcript Variant
SLC22A23 transcript variant 9	NM_001382320.1:c.	N/A	Genic Downstream Transcript Variant
SLC22A23 transcript variant 10	NM_001382321.1:c.	N/A	Genic Downstream 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.1386-991… XM_011514801.3:c.1386-991C>T	N/A	Intron Variant
SLC22A23 transcript variant X5	XM_017011180.2:c.792-991C… XM_017011180.2:c.792-991C>T	N/A	Intron Variant
SLC22A23 transcript variant X7	XM_017011184.2:c.369-991C… XM_017011184.2:c.369-991C>T	N/A	Intron Variant
SLC22A23 transcript variant X11	XM_017011186.2:c.471-991C… XM_017011186.2:c.471-991C>T	N/A	Intron Variant
SLC22A23 transcript variant X6	XM_047419241.1:c.369-991C… XM_047419241.1:c.369-991C>T	N/A	Intron Variant
SLC22A23 transcript variant X8	XM_047419242.1:c.369-991C… XM_047419242.1:c.369-991C>T	N/A	Intron Variant
SLC22A23 transcript variant X9	XM_047419243.1:c.369-991C… XM_047419243.1:c.369-991C>T	N/A	Intron Variant
SLC22A23 transcript variant X3	XM_017011183.2:c.	N/A	Genic Downstream Transcript Variant
SLC22A23 transcript variant X4	XM_017011185.3:c.	N/A	Genic Downstream 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	Genic Downstream Transcript Variant
SLC22A23 transcript variant X10	XR_007059328.1:n.	N/A	Genic Downstream Transcript Variant

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

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
GRCh38.p14 chr 6	NC_000006.12:g.3288082=	NC_000006.12:g.3288082G>A
GRCh37.p13 chr 6	NC_000006.11:g.3288316=	NC_000006.11:g.3288316G>A
SLC22A23 transcript variant 3	NM_001286455.1:c.471-991=	NM_001286455.1:c.471-991C>T
SLC22A23 transcript variant 6	NM_001382317.1:c.1314-991=	NM_001382317.1:c.1314-991C>T
SLC22A23 transcript variant 7	NM_001382318.1:c.423-991=	NM_001382318.1:c.423-991C>T
SLC22A23 transcript variant 8	NM_001382319.1:c.423-991=	NM_001382319.1:c.423-991C>T
SLC22A23 transcript variant 1	NM_015482.1:c.1314-991=	NM_015482.1:c.1314-991C>T
SLC22A23 transcript variant 1	NM_015482.2:c.1314-991=	NM_015482.2:c.1314-991C>T
SLC22A23 transcript variant 2	NM_021945.5:c.471-991=	NM_021945.5:c.471-991C>T
SLC22A23 transcript variant 2	NM_021945.6:c.471-991=	NM_021945.6:c.471-991C>T
SLC22A23 transcript variant X1	XM_005249285.1:c.1314-991=	XM_005249285.1:c.1314-991C>T
SLC22A23 transcript variant X2	XM_005249286.1:c.471-991=	XM_005249286.1:c.471-991C>T
SLC22A23 transcript variant X1	XM_011514801.3:c.1386-991=	XM_011514801.3:c.1386-991C>T
SLC22A23 transcript variant X5	XM_017011180.2:c.792-991=	XM_017011180.2:c.792-991C>T
SLC22A23 transcript variant X7	XM_017011184.2:c.369-991=	XM_017011184.2:c.369-991C>T
SLC22A23 transcript variant X11	XM_017011186.2:c.471-991=	XM_017011186.2:c.471-991C>T
SLC22A23 transcript variant X6	XM_047419241.1:c.369-991=	XM_047419241.1:c.369-991C>T
SLC22A23 transcript variant X8	XM_047419242.1:c.369-991=	XM_047419242.1:c.369-991C>T
SLC22A23 transcript variant X9	XM_047419243.1:c.369-991=	XM_047419243.1:c.369-991C>T

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#.

26 SubSNP, 13 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	1000GENOMES	ss233297454	Jul 14, 2010 (132)
2	EVA-GONL	ss982518838	Aug 21, 2014 (142)
3	1000GENOMES	ss1318729251	Aug 21, 2014 (142)
4	EVA_DECODE	ss1592064666	Apr 01, 2015 (144)
5	EVA_UK10K_ALSPAC	ss1614816850	Apr 01, 2015 (144)
6	EVA_UK10K_TWINSUK	ss1657810883	Apr 01, 2015 (144)
7	USC_VALOUEV	ss2151664770	Dec 20, 2016 (150)
8	HUMAN_LONGEVITY	ss2281292932	Dec 20, 2016 (150)
9	ILLUMINA	ss2711058178	Nov 08, 2017 (151)
10	GNOMAD	ss2835118367	Nov 08, 2017 (151)
11	SWEGEN	ss2998416616	Nov 08, 2017 (151)
12	EGCUT_WGS	ss3666340016	Jul 13, 2019 (153)
13	EVA_DECODE	ss3716460614	Jul 13, 2019 (153)
14	KHV_HUMAN_GENOMES	ss3807696792	Jul 13, 2019 (153)
15	SGDP_PRJ	ss3863789747	Apr 26, 2020 (154)
16	TOPMED	ss4691659971	Apr 26, 2021 (155)
17	TOMMO_GENOMICS	ss5175887795	Apr 26, 2021 (155)
18	1000G_HIGH_COVERAGE	ss5267186094	Oct 13, 2022 (156)
19	EVA	ss5363420145	Oct 13, 2022 (156)
20	HUGCELL_USP	ss5464999604	Oct 13, 2022 (156)
21	1000G_HIGH_COVERAGE	ss5552511262	Oct 13, 2022 (156)
22	SANFORD_IMAGENETICS	ss5639643770	Oct 13, 2022 (156)
23	TOMMO_GENOMICS	ss5713476066	Oct 13, 2022 (156)
24	EVA	ss5841707854	Oct 13, 2022 (156)
25	EVA	ss5882407040	Oct 13, 2022 (156)
26	EVA	ss5968136590	Oct 13, 2022 (156)
27	1000Genomes	NC_000006.11 - 3288316	Oct 12, 2018 (152)
28	1000Genomes_30x	NC_000006.12 - 3288082	Oct 13, 2022 (156)
29	The Avon Longitudinal Study of Parents and Children	NC_000006.11 - 3288316	Oct 12, 2018 (152)
30	Genetic variation in the Estonian population	NC_000006.11 - 3288316	Oct 12, 2018 (152)
31	gnomAD - Genomes	NC_000006.12 - 3288082	Apr 26, 2021 (155)
32	Genome of the Netherlands Release 5	NC_000006.11 - 3288316	Apr 26, 2020 (154)
33	SGDP_PRJ	NC_000006.11 - 3288316	Apr 26, 2020 (154)
34	Siberian	NC_000006.11 - 3288316	Apr 26, 2020 (154)
35	8.3KJPN	NC_000006.11 - 3288316	Apr 26, 2021 (155)
36	14KJPN	NC_000006.12 - 3288082	Oct 13, 2022 (156)
37	TopMed	NC_000006.12 - 3288082	Apr 26, 2021 (155)
38	UK 10K study - Twins	NC_000006.11 - 3288316	Oct 12, 2018 (152)
39	ALFA	NC_000006.12 - 3288082	Apr 26, 2021 (155)

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
ss1592064666	NC_000006.10:3233314:G:A	NC_000006.12:3288081:G:A	(self)
30462165, 16954690, 12078264, 7525567, 15806727, 4181124, 33857102, 16954690, ss233297454, ss982518838, ss1318729251, ss1614816850, ss1657810883, ss2151664770, ss2711058178, ss2835118367, ss2998416616, ss3666340016, ss3863789747, ss5175887795, ss5363420145, ss5639643770, ss5841707854, ss5968136590	NC_000006.11:3288315:G:A	NC_000006.12:3288081:G:A	(self)
40037197, 215395700, 47313170, 529037529, 12485847052, ss2281292932, ss3716460614, ss3807696792, ss4691659971, ss5267186094, ss5464999604, ss5552511262, ss5713476066, ss5882407040	NC_000006.12:3288081:G:A	NC_000006.12:3288081:G:A	(self)

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

No publications for rs74671366

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.

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dbSNP Short Genetic Variations

Welcome to the Reference SNP (rs) Report

Reference SNP (rs) Report

rs74671366