Name: rs13193224
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.

rs13193224

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr6:31349800 (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 / G>T
Variation Type: SNV Single Nucleotide Variation
Frequency: T=0.141150 (37361/264690, TOPMED)
T=0.07732 (2185/28258, 14KJPN)
T=0.07852 (1314/16734, 8.3KJPN) (+ 12 more)
T=0.07582 (1215/16024, ALFA)
T=0.1344 (861/6404, 1000G_30x)
T=0.1388 (695/5008, 1000G)
T=0.0922 (270/2930, KOREAN)
T=0.128 (128/998, GoNL)
T=0.078 (47/600, NorthernSweden)
T=0.269 (58/216, Qatari)
T=0.163 (34/208, Vietnamese)
G=0.446 (74/166, SGDP_PRJ)
T=0.15 (6/40, GENOME_DK)
G=0.50 (10/20, Siberian)
T=0.50 (10/20, Siberian)

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	16024	G=0.92418	A=0.00000, T=0.07582
European	Sub	12300	G=0.90878	A=0.00000, T=0.09122
African	Sub	2492	G=0.9767	A=0.0000, T=0.0233
African Others	Sub	100	G=0.97	A=0.00, T=0.03
African American	Sub	2392	G=0.9770	A=0.0000, T=0.0230
Asian	Sub	64	G=0.98	A=0.00, T=0.02
East Asian	Sub	54	G=0.98	A=0.00, T=0.02
Other Asian	Sub	10	G=1.0	A=0.0, T=0.0
Latin American 1	Sub	106	G=1.000	A=0.000, T=0.000
Latin American 2	Sub	426	G=1.000	A=0.000, T=0.000
South Asian	Sub	70	G=1.00	A=0.00, T=0.00
Other	Sub	566	G=0.940	A=0.000, T=0.060

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=0.858850	T=0.141150
14KJPN	JAPANESE	Study-wide	28258	G=0.92268	T=0.07732
8.3KJPN	JAPANESE	Study-wide	16734	G=0.92148	T=0.07852
Allele Frequency Aggregator	Total	Global	16024	G=0.92418	A=0.00000, T=0.07582
Allele Frequency Aggregator	European	Sub	12300	G=0.90878	A=0.00000, T=0.09122
Allele Frequency Aggregator	African	Sub	2492	G=0.9767	A=0.0000, T=0.0233
Allele Frequency Aggregator	Other	Sub	566	G=0.940	A=0.000, T=0.060
Allele Frequency Aggregator	Latin American 2	Sub	426	G=1.000	A=0.000, T=0.000
Allele Frequency Aggregator	Latin American 1	Sub	106	G=1.000	A=0.000, T=0.000
Allele Frequency Aggregator	South Asian	Sub	70	G=1.00	A=0.00, T=0.00
Allele Frequency Aggregator	Asian	Sub	64	G=0.98	A=0.00, T=0.02
1000Genomes_30x	Global	Study-wide	6404	G=0.8656	T=0.1344
1000Genomes_30x	African	Sub	1786	G=0.9211	T=0.0789
1000Genomes_30x	Europe	Sub	1266	G=0.8468	T=0.1532
1000Genomes_30x	South Asian	Sub	1202	G=0.7912	T=0.2088
1000Genomes_30x	East Asian	Sub	1170	G=0.8778	T=0.1222
1000Genomes_30x	American	Sub	980	G=0.865	T=0.135
1000Genomes	Global	Study-wide	5008	G=0.8612	T=0.1388
1000Genomes	African	Sub	1322	G=0.9145	T=0.0855
1000Genomes	East Asian	Sub	1008	G=0.8770	T=0.1230
1000Genomes	Europe	Sub	1006	G=0.8429	T=0.1571
1000Genomes	South Asian	Sub	978	G=0.780	T=0.220
1000Genomes	American	Sub	694	G=0.878	T=0.122
KOREAN population from KRGDB	KOREAN	Study-wide	2930	G=0.9078	T=0.0922
Genome of the Netherlands Release 5	Genome of the Netherlands	Study-wide	998	G=0.872	T=0.128
Northern Sweden	ACPOP	Study-wide	600	G=0.922	T=0.078
Qatari	Global	Study-wide	216	G=0.731	T=0.269
A Vietnamese Genetic Variation Database	Global	Study-wide	208	G=0.837	T=0.163
SGDP_PRJ	Global	Study-wide	166	G=0.446	A=0.006, T=0.548
The Danish reference pan genome	Danish	Study-wide	40	G=0.85	T=0.15
Siberian	Global	Study-wide	20	G=0.50	T=0.50

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.31349800G>A
GRCh38.p14 chr 6	NC_000006.12:g.31349800G>T
GRCh37.p13 chr 6	NC_000006.11:g.31317577G>A
GRCh37.p13 chr 6	NC_000006.11:g.31317577G>T
GRCh38.p14 chr 6 alt locus HSCHR6_MHC_COX_CTG1	NT_113891.3:g.2830157G>A
GRCh38.p14 chr 6 alt locus HSCHR6_MHC_COX_CTG1	NT_113891.3:g.2830157G>T
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_COX_CTG1	NT_113891.2:g.2830263G>A
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_COX_CTG1	NT_113891.2:g.2830263G>T
GRCh38.p14 chr 6 alt locus HSCHR6_MHC_QBL_CTG1	NT_167248.2:g.2605455G>A
GRCh38.p14 chr 6 alt locus HSCHR6_MHC_QBL_CTG1	NT_167248.2:g.2605455G>T
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_QBL_CTG1	NT_167248.1:g.2611051G>A
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_QBL_CTG1	NT_167248.1:g.2611051G>T
GRCh38.p14 chr 6 alt locus HSCHR6_MHC_DBB_CTG1	NT_167245.2:g.2597324T>G
GRCh38.p14 chr 6 alt locus HSCHR6_MHC_DBB_CTG1	NT_167245.2:g.2597324T>A
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_DBB_CTG1	NT_167245.1:g.2602909T>G
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_DBB_CTG1	NT_167245.1:g.2602909T>A
GRCh38.p14 chr 6 alt locus HSCHR6_MHC_SSTO_CTG1	NT_167249.2:g.2651996G>A
GRCh38.p14 chr 6 alt locus HSCHR6_MHC_SSTO_CTG1	NT_167249.2:g.2651996G>T
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_SSTO_CTG1	NT_167249.1:g.2651294G>A
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_SSTO_CTG1	NT_167249.1:g.2651294G>T
GRCh38.p14 chr 6 alt locus HSCHR6_MHC_MANN_CTG1	NT_167246.2:g.2658411G>A
GRCh38.p14 chr 6 alt locus HSCHR6_MHC_MANN_CTG1	NT_167246.2:g.2658411G>T
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_MANN_CTG1	NT_167246.1:g.2664031G>A
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_MANN_CTG1	NT_167246.1:g.2664031G>T
GRCh38.p14 chr 6 alt locus HSCHR6_MHC_MCF_CTG1	NT_167247.2:g.2691732G>A
GRCh38.p14 chr 6 alt locus HSCHR6_MHC_MCF_CTG1	NT_167247.2:g.2691732G>T
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_MCF_CTG1	NT_167247.1:g.2697317G>A
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_MCF_CTG1	NT_167247.1:g.2697317G>T

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	T
GRCh38.p14 chr 6	NC_000006.12:g.31349800=	NC_000006.12:g.31349800G>A	NC_000006.12:g.31349800G>T
GRCh37.p13 chr 6	NC_000006.11:g.31317577=	NC_000006.11:g.31317577G>A	NC_000006.11:g.31317577G>T
GRCh38.p14 chr 6 alt locus HSCHR6_MHC_COX_CTG1	NT_113891.3:g.2830157=	NT_113891.3:g.2830157G>A	NT_113891.3:g.2830157G>T
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_COX_CTG1	NT_113891.2:g.2830263=	NT_113891.2:g.2830263G>A	NT_113891.2:g.2830263G>T
GRCh38.p14 chr 6 alt locus HSCHR6_MHC_QBL_CTG1	NT_167248.2:g.2605455=	NT_167248.2:g.2605455G>A	NT_167248.2:g.2605455G>T
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_QBL_CTG1	NT_167248.1:g.2611051=	NT_167248.1:g.2611051G>A	NT_167248.1:g.2611051G>T
GRCh38.p14 chr 6 alt locus HSCHR6_MHC_DBB_CTG1	NT_167245.2:g.2597324T>G	NT_167245.2:g.2597324T>A	NT_167245.2:g.2597324=
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_DBB_CTG1	NT_167245.1:g.2602909T>G	NT_167245.1:g.2602909T>A	NT_167245.1:g.2602909=
GRCh38.p14 chr 6 alt locus HSCHR6_MHC_SSTO_CTG1	NT_167249.2:g.2651996=	NT_167249.2:g.2651996G>A	NT_167249.2:g.2651996G>T
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_SSTO_CTG1	NT_167249.1:g.2651294=	NT_167249.1:g.2651294G>A	NT_167249.1:g.2651294G>T
GRCh38.p14 chr 6 alt locus HSCHR6_MHC_MANN_CTG1	NT_167246.2:g.2658411=	NT_167246.2:g.2658411G>A	NT_167246.2:g.2658411G>T
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_MANN_CTG1	NT_167246.1:g.2664031=	NT_167246.1:g.2664031G>A	NT_167246.1:g.2664031G>T
GRCh38.p14 chr 6 alt locus HSCHR6_MHC_MCF_CTG1	NT_167247.2:g.2691732=	NT_167247.2:g.2691732G>A	NT_167247.2:g.2691732G>T
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_MCF_CTG1	NT_167247.1:g.2697317=	NT_167247.1:g.2697317G>A	NT_167247.1:g.2697317G>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#.

53 SubSNP, 16 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	SSAHASNP	ss22380088	Apr 05, 2004 (121)
2	SSAHASNP	ss35472220	May 24, 2005 (125)
3	SI_MHC_SNP	ss35524632	May 24, 2005 (125)
4	ABI	ss42702817	Mar 15, 2006 (126)
5	HUMANGENOME_JCVI	ss98379534	Feb 05, 2009 (130)
6	ENSEMBL	ss142703543	Dec 01, 2009 (131)
7	1000GENOMES	ss233396255	Jul 14, 2010 (137)
8	1000GENOMES	ss240467367	Jul 15, 2010 (137)
9	BL	ss254181916	May 09, 2011 (137)
10	GMI	ss278724074	May 04, 2012 (137)
11	PJP	ss293824640	May 09, 2011 (137)
12	TISHKOFF	ss559111667	Apr 25, 2013 (138)
13	SSMP	ss653031840	Apr 25, 2013 (138)
14	EVA-GONL	ss982761798	Aug 21, 2014 (142)
15	JMKIDD_LAB	ss1073503195	Aug 21, 2014 (142)
16	1000GENOMES	ss1319550453	Aug 21, 2014 (142)
17	EVA_GENOME_DK	ss1581604394	Apr 01, 2015 (144)
18	EVA_DECODE	ss1592306540	Apr 01, 2015 (144)
19	EVA_DECODE	ss1592306541	Apr 01, 2015 (144)
20	HAMMER_LAB	ss1804355931	Sep 08, 2015 (146)
21	WEILL_CORNELL_DGM	ss1926013662	Feb 12, 2016 (147)
22	GENOMED	ss1970355756	Jul 19, 2016 (147)
23	JJLAB	ss2023639055	Sep 14, 2016 (149)
24	USC_VALOUEV	ss2151805007	Dec 20, 2016 (150)
25	HUMAN_LONGEVITY	ss2282937099	Dec 20, 2016 (150)
26	GRF	ss2707398372	Nov 08, 2017 (151)
27	SWEGEN	ss2998790122	Nov 08, 2017 (151)
28	BIOINF_KMB_FNS_UNIBA	ss3025606121	Nov 08, 2017 (151)
29	URBANLAB	ss3648308764	Oct 12, 2018 (152)
30	ACPOP	ss3733357356	Jul 13, 2019 (153)
31	EVA	ss3764817943	Jul 13, 2019 (153)
32	PACBIO	ss3785423804	Jul 13, 2019 (153)
33	PACBIO	ss3790783236	Jul 13, 2019 (153)
34	PACBIO	ss3795660723	Jul 13, 2019 (153)
35	KHV_HUMAN_GENOMES	ss3807973144	Jul 13, 2019 (153)
36	EVA	ss3829829705	Apr 26, 2020 (154)
37	SGDP_PRJ	ss3864246999	Apr 26, 2020 (154)
38	KRGDB	ss3911022385	Apr 26, 2020 (154)
39	VINODS	ss4025208843	Apr 26, 2021 (155)
40	VINODS	ss4025227710	Apr 26, 2021 (155)
41	TOPMED	ss4698350298	Apr 26, 2021 (155)
42	TOMMO_GENOMICS	ss5176826910	Apr 26, 2021 (155)
43	1000G_HIGH_COVERAGE	ss5267929152	Oct 13, 2022 (156)
44	EVA	ss5364713507	Oct 13, 2022 (156)
45	EVA	ss5508425357	Oct 13, 2022 (156)
46	1000G_HIGH_COVERAGE	ss5553583773	Oct 13, 2022 (156)
47	SANFORD_IMAGENETICS	ss5640083440	Oct 13, 2022 (156)
48	TOMMO_GENOMICS	ss5714679091	Oct 13, 2022 (156)
49	YY_MCH	ss5807302772	Oct 13, 2022 (156)
50	EVA	ss5842021567	Oct 13, 2022 (156)
51	EVA	ss5855281383	Oct 13, 2022 (156)
52	EVA	ss5883236917	Oct 13, 2022 (156)
53	EVA	ss5968585853	Oct 13, 2022 (156)
54	1000Genomes	NC_000006.11 - 31317577	Oct 12, 2018 (152)
55	1000Genomes_30x	NC_000006.12 - 31349800	Oct 13, 2022 (156)
56	The Danish reference pan genome	NC_000006.11 - 31317577	Apr 26, 2020 (154)
57	gnomAD - Genomes Submission ignored due to conflicting rows: Row 221177250 (NC_000006.12:31349799:G:A 2/67536) Row 221177251 (NC_000006.12:31349799:G:T 19370/67504)	-	Apr 26, 2021 (155)
58	gnomAD - Genomes Submission ignored due to conflicting rows: Row 221177250 (NC_000006.12:31349799:G:A 2/67536) Row 221177251 (NC_000006.12:31349799:G:T 19370/67504)	-	Apr 26, 2021 (155)
59	Genome of the Netherlands Release 5	NC_000006.11 - 31317577	Apr 26, 2020 (154)
60	KOREAN population from KRGDB	NC_000006.11 - 31317577	Apr 26, 2020 (154)
61	Northern Sweden	NC_000006.11 - 31317577	Jul 13, 2019 (153)
62	Qatari	NC_000006.11 - 31317577	Apr 26, 2020 (154)
63	SGDP_PRJ	NC_000006.11 - 31317577	Apr 26, 2020 (154)
64	Siberian	NC_000006.11 - 31317577	Apr 26, 2020 (154)
65	8.3KJPN	NC_000006.11 - 31317577	Apr 26, 2021 (155)
66	14KJPN	NC_000006.12 - 31349800	Oct 13, 2022 (156)
67	TopMed	NC_000006.12 - 31349800	Apr 26, 2021 (155)
68	A Vietnamese Genetic Variation Database	NC_000006.11 - 31317577	Jul 13, 2019 (153)
69	ALFA	NC_000006.12 - 31349800	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).

Associated ID	History Updated (Build)
rs116121831	May 04, 2012 (137)
rs117466284	Aug 16, 2010 (132)

Added to this RefSNP Cluster:

Submission IDs	Observation SPDI	Canonical SPDI	Source RSIDs
ss1592306540	NC_000006.10:31425555:G:A	NC_000006.12:31349799:G:A	(self)
16263979, ss3864246999	NC_000006.11:31317576:G:A	NC_000006.12:31349799:G:A	(self)
15659692983	NC_000006.12:31349799:G:A	NC_000006.12:31349799:G:A	(self)
ss35472220	NC_000006.9:31425555:G:T	NC_000006.12:31349799:G:T	(self)
ss254181916, ss278724074, ss293824640, ss1592306541	NC_000006.10:31425555:G:T	NC_000006.12:31349799:G:T	(self)
31317524, 7769333, 7760945, 18199779, 6642221, 8055592, 16263979, 4321361, 34796217, 3871417, ss233396255, ss240467367, ss559111667, ss653031840, ss982761798, ss1073503195, ss1319550453, ss1581604394, ss1804355931, ss1926013662, ss1970355756, ss2023639055, ss2151805007, ss2707398372, ss2998790122, ss3733357356, ss3764817943, ss3785423804, ss3790783236, ss3795660723, ss3829829705, ss3864246999, ss3911022385, ss5176826910, ss5364713507, ss5508425357, ss5640083440, ss5842021567, ss5968585853	NC_000006.11:31317576:G:T	NC_000006.12:31349799:G:T	(self)
41109708, 48516195, 535727856, 15659692983, ss2282937099, ss3025606121, ss3648308764, ss3807973144, ss4698350298, ss5267929152, ss5553583773, ss5714679091, ss5807302772, ss5855281383, ss5883236917	NC_000006.12:31349799:G:T	NC_000006.12:31349799:G:T	(self)
ss22380088	NT_007592.13:22172037:G:T	NC_000006.12:31349799:G:T	(self)
ss35524632, ss42702817, ss98379534, ss142703543	NT_007592.15:31257576:G:T	NC_000006.12:31349799:G:T	(self)
ss4025208843	NT_167245.2:2597323:T:T	NC_000006.12:31349799:G:T	(self)
ss4025227710	NT_167246.2:2658410:G:T	NC_000006.12:31349799:G:T	(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 rs13193224

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.

Choose placement

dbSNP Short Genetic Variations

Welcome to the Reference SNP (rs) Report

Reference SNP (rs) Report

rs13193224