Name: rs1403830
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.

rs1403830

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr2:215058191 (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: A>C / A>G / A>T
Variation Type: SNV Single Nucleotide Variation
Frequency: A=0.346190 (91633/264690, TOPMED)
A=0.351309 (49099/139760, GnomAD)
A=0.22324 (6308/28256, 14KJPN) (+ 16 more)
A=0.36861 (6963/18890, ALFA)
A=0.22178 (3717/16760, 8.3KJPN)
A=0.3440 (2203/6404, 1000G_30x)
A=0.3490 (1748/5008, 1000G)
A=0.3806 (1705/4480, Estonian)
A=0.4107 (1583/3854, ALSPAC)
A=0.4091 (1517/3708, TWINSUK)
A=0.2085 (611/2930, KOREAN)
A=0.2249 (412/1832, Korea1K)
A=0.411 (410/998, GoNL)
A=0.398 (239/600, NorthernSweden)
A=0.260 (115/442, SGDP_PRJ)
A=0.431 (93/216, Qatari)
A=0.375 (81/216, Vietnamese)
A=0.25 (13/52, Siberian)
A=0.35 (14/40, GENOME_DK)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: ABCA12 : 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	A=0.36861	T=0.63139
European	Sub	14286	A=0.39311	T=0.60689
African	Sub	2946	A=0.2383	T=0.7617
African Others	Sub	114	A=0.149	T=0.851
African American	Sub	2832	A=0.2419	T=0.7581
Asian	Sub	112	A=0.223	T=0.777
East Asian	Sub	86	A=0.22	T=0.78
Other Asian	Sub	26	A=0.23	T=0.77
Latin American 1	Sub	146	A=0.342	T=0.658
Latin American 2	Sub	610	A=0.464	T=0.536
South Asian	Sub	98	A=0.41	T=0.59
Other	Sub	692	A=0.357	T=0.643

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	A=0.346190	T=0.653810
gnomAD - Genomes	Global	Study-wide	139760	A=0.351309	T=0.648691
gnomAD - Genomes	European	Sub	75722	A=0.40278	T=0.59722
gnomAD - Genomes	African	Sub	41886	A=0.23378	T=0.76622
gnomAD - Genomes	American	Sub	13600	A=0.43699	T=0.56301
gnomAD - Genomes	Ashkenazi Jewish	Sub	3322	A=0.3847	T=0.6153
gnomAD - Genomes	East Asian	Sub	3082	A=0.2706	T=0.7294
gnomAD - Genomes	Other	Sub	2148	A=0.3506	T=0.6494
14KJPN	JAPANESE	Study-wide	28256	A=0.22324	T=0.77676
Allele Frequency Aggregator	Total	Global	18890	A=0.36861	T=0.63139
Allele Frequency Aggregator	European	Sub	14286	A=0.39311	T=0.60689
Allele Frequency Aggregator	African	Sub	2946	A=0.2383	T=0.7617
Allele Frequency Aggregator	Other	Sub	692	A=0.357	T=0.643
Allele Frequency Aggregator	Latin American 2	Sub	610	A=0.464	T=0.536
Allele Frequency Aggregator	Latin American 1	Sub	146	A=0.342	T=0.658
Allele Frequency Aggregator	Asian	Sub	112	A=0.223	T=0.777
Allele Frequency Aggregator	South Asian	Sub	98	A=0.41	T=0.59
8.3KJPN	JAPANESE	Study-wide	16760	A=0.22178	T=0.77822
1000Genomes_30x	Global	Study-wide	6404	A=0.3440	T=0.6560
1000Genomes_30x	African	Sub	1786	A=0.1781	T=0.8219
1000Genomes_30x	Europe	Sub	1266	A=0.3736	T=0.6264
1000Genomes_30x	South Asian	Sub	1202	A=0.5507	T=0.4493
1000Genomes_30x	East Asian	Sub	1170	A=0.2915	T=0.7085
1000Genomes_30x	American	Sub	980	A=0.417	T=0.583
1000Genomes	Global	Study-wide	5008	A=0.3490	T=0.6510
1000Genomes	African	Sub	1322	A=0.1823	T=0.8177
1000Genomes	East Asian	Sub	1008	A=0.2927	T=0.7073
1000Genomes	Europe	Sub	1006	A=0.3867	T=0.6133
1000Genomes	South Asian	Sub	978	A=0.540	T=0.460
1000Genomes	American	Sub	694	A=0.425	T=0.575
Genetic variation in the Estonian population	Estonian	Study-wide	4480	A=0.3806	T=0.6194
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	A=0.4107	T=0.5893
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	A=0.4091	T=0.5909
KOREAN population from KRGDB	KOREAN	Study-wide	2930	A=0.2085	C=0.0000, G=0.0000, T=0.7915
Korean Genome Project	KOREAN	Study-wide	1832	A=0.2249	T=0.7751
Genome of the Netherlands Release 5	Genome of the Netherlands	Study-wide	998	A=0.411	T=0.589
Northern Sweden	ACPOP	Study-wide	600	A=0.398	T=0.602
SGDP_PRJ	Global	Study-wide	442	A=0.260	T=0.740
Qatari	Global	Study-wide	216	A=0.431	T=0.569
A Vietnamese Genetic Variation Database	Global	Study-wide	216	A=0.375	T=0.625
Siberian	Global	Study-wide	52	A=0.25	T=0.75
The Danish reference pan genome	Danish	Study-wide	40	A=0.35	T=0.65

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 2	NC_000002.12:g.215058191A>C
GRCh38.p14 chr 2	NC_000002.12:g.215058191A>G
GRCh38.p14 chr 2	NC_000002.12:g.215058191A>T
GRCh37.p13 chr 2	NC_000002.11:g.215922915A>C
GRCh37.p13 chr 2	NC_000002.11:g.215922915A>G
GRCh37.p13 chr 2	NC_000002.11:g.215922915A>T
ABCA12 RefSeqGene	NG_007074.2:g.85435T>G
ABCA12 RefSeqGene	NG_007074.2:g.85435T>C
ABCA12 RefSeqGene	NG_007074.2:g.85435T>A
ABCA12 RefSeqGene	NG_007074.1:g.85237T>G
ABCA12 RefSeqGene	NG_007074.1:g.85237T>C
ABCA12 RefSeqGene	NG_007074.1:g.85237T>A

Gene: ABCA12, ATP binding cassette subfamily A member 12 (minus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
ABCA12 transcript variant 1	NM_173076.3:c.318-3527T>G	N/A	Intron Variant
ABCA12 transcript variant 2	NM_015657.4:c.	N/A	Genic Upstream Transcript Variant
ABCA12 transcript variant 3	NR_103740.2:n.	N/A	Intron Variant
ABCA12 transcript variant X1	XM_011510951.3:c.318-3527… XM_011510951.3:c.318-3527T>G	N/A	Intron 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	A=	C	G	T
GRCh38.p14 chr 2	NC_000002.12:g.215058191=	NC_000002.12:g.215058191A>C	NC_000002.12:g.215058191A>G	NC_000002.12:g.215058191A>T
GRCh37.p13 chr 2	NC_000002.11:g.215922915=	NC_000002.11:g.215922915A>C	NC_000002.11:g.215922915A>G	NC_000002.11:g.215922915A>T
ABCA12 RefSeqGene	NG_007074.2:g.85435=	NG_007074.2:g.85435T>G	NG_007074.2:g.85435T>C	NG_007074.2:g.85435T>A
ABCA12 RefSeqGene	NG_007074.1:g.85237=	NG_007074.1:g.85237T>G	NG_007074.1:g.85237T>C	NG_007074.1:g.85237T>A
ABCA12 transcript variant 1	NM_173076.2:c.318-3527=	NM_173076.2:c.318-3527T>G	NM_173076.2:c.318-3527T>C	NM_173076.2:c.318-3527T>A
ABCA12 transcript variant 1	NM_173076.3:c.318-3527=	NM_173076.3:c.318-3527T>G	NM_173076.3:c.318-3527T>C	NM_173076.3:c.318-3527T>A
ABCA12 transcript variant X1	XM_011510951.3:c.318-3527=	XM_011510951.3:c.318-3527T>G	XM_011510951.3:c.318-3527T>C	XM_011510951.3:c.318-3527T>A

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#.

75 SubSNP, 19 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	TSC-CSHL	ss2202526	Oct 23, 2000 (88)
2	CSHL-HAPMAP	ss19411770	Feb 27, 2004 (120)
3	SSAHASNP	ss21571992	Apr 05, 2004 (121)
4	ABI	ss41823501	Mar 13, 2006 (126)
5	HGSV	ss85859976	Dec 16, 2007 (130)
6	BCMHGSC_JDW	ss91541482	Mar 24, 2008 (129)
7	HUMANGENOME_JCVI	ss97120578	Feb 06, 2009 (130)
8	BGI	ss106159976	Feb 06, 2009 (130)
9	1000GENOMES	ss110740918	Jan 25, 2009 (130)
10	1000GENOMES	ss111635984	Jan 25, 2009 (130)
11	ENSEMBL	ss135973405	Dec 01, 2009 (131)
12	ENSEMBL	ss138627889	Dec 01, 2009 (131)
13	COMPLETE_GENOMICS	ss165459159	Jul 04, 2010 (132)
14	COMPLETE_GENOMICS	ss165895988	Jul 04, 2010 (132)
15	COMPLETE_GENOMICS	ss167568955	Jul 04, 2010 (132)
16	BUSHMAN	ss201722239	Jul 04, 2010 (132)
17	BCM-HGSC-SUB	ss205844664	Jul 04, 2010 (132)
18	1000GENOMES	ss219805579	Jul 14, 2010 (132)
19	1000GENOMES	ss231581842	Jul 14, 2010 (132)
20	1000GENOMES	ss239041556	Jul 15, 2010 (132)
21	BL	ss253868592	May 09, 2011 (134)
22	GMI	ss276893369	May 04, 2012 (137)
23	GMI	ss284539324	Apr 25, 2013 (138)
24	PJP	ss292485193	May 09, 2011 (134)
25	TISHKOFF	ss556211160	Apr 25, 2013 (138)
26	SSMP	ss649877941	Apr 25, 2013 (138)
27	EVA-GONL	ss977948362	Aug 21, 2014 (142)
28	JMKIDD_LAB	ss1069931543	Aug 21, 2014 (142)
29	1000GENOMES	ss1301598776	Aug 21, 2014 (142)
30	DDI	ss1428907233	Apr 01, 2015 (144)
31	EVA_GENOME_DK	ss1579318350	Apr 01, 2015 (144)
32	EVA_DECODE	ss1587403269	Apr 01, 2015 (144)
33	EVA_UK10K_ALSPAC	ss1605767498	Apr 01, 2015 (144)
34	EVA_UK10K_TWINSUK	ss1648761531	Apr 01, 2015 (144)
35	HAMMER_LAB	ss1798335613	Sep 08, 2015 (146)
36	WEILL_CORNELL_DGM	ss1921192755	Feb 12, 2016 (147)
37	GENOMED	ss1969021986	Jul 19, 2016 (147)
38	JJLAB	ss2021144246	Sep 14, 2016 (149)
39	USC_VALOUEV	ss2149205847	Dec 20, 2016 (150)
40	HUMAN_LONGEVITY	ss2239053397	Dec 20, 2016 (150)
41	SYSTEMSBIOZJU	ss2625071496	Nov 08, 2017 (151)
42	GRF	ss2703854187	Nov 08, 2017 (151)
43	GNOMAD	ss2786199505	Nov 08, 2017 (151)
44	SWEGEN	ss2991338983	Nov 08, 2017 (151)
45	BIOINF_KMB_FNS_UNIBA	ss3024330220	Nov 08, 2017 (151)
46	CSHL	ss3344735725	Nov 08, 2017 (151)
47	URBANLAB	ss3647271457	Oct 11, 2018 (152)
48	EGCUT_WGS	ss3659234098	Jul 13, 2019 (153)
49	EVA_DECODE	ss3705999082	Jul 13, 2019 (153)
50	ACPOP	ss3729361722	Jul 13, 2019 (153)
51	EVA	ss3758068857	Jul 13, 2019 (153)
52	PACBIO	ss3784150992	Jul 13, 2019 (153)
53	PACBIO	ss3789689592	Jul 13, 2019 (153)
54	PACBIO	ss3794562769	Jul 13, 2019 (153)
55	KHV_HUMAN_GENOMES	ss3802432327	Jul 13, 2019 (153)
56	EVA	ss3827500241	Apr 25, 2020 (154)
57	EVA	ss3837169656	Apr 25, 2020 (154)
58	EVA	ss3842591372	Apr 25, 2020 (154)
59	SGDP_PRJ	ss3854569277	Apr 25, 2020 (154)
60	KRGDB	ss3900286291	Apr 25, 2020 (154)
61	KOGIC	ss3950058980	Apr 25, 2020 (154)
62	TOPMED	ss4544248561	Apr 26, 2021 (155)
63	TOMMO_GENOMICS	ss5156443107	Apr 26, 2021 (155)
64	1000G_HIGH_COVERAGE	ss5251992071	Oct 12, 2022 (156)
65	EVA	ss5335959831	Oct 12, 2022 (156)
66	HUGCELL_USP	ss5451606364	Oct 12, 2022 (156)
67	EVA	ss5506794780	Oct 12, 2022 (156)
68	1000G_HIGH_COVERAGE	ss5529322160	Oct 12, 2022 (156)
69	SANFORD_IMAGENETICS	ss5630929798	Oct 12, 2022 (156)
70	TOMMO_GENOMICS	ss5687310546	Oct 12, 2022 (156)
71	YY_MCH	ss5803211149	Oct 12, 2022 (156)
72	EVA	ss5821575698	Oct 12, 2022 (156)
73	EVA	ss5852946615	Oct 12, 2022 (156)
74	EVA	ss5934658193	Oct 12, 2022 (156)
75	EVA	ss5957184190	Oct 12, 2022 (156)
76	1000Genomes	NC_000002.11 - 215922915	Oct 11, 2018 (152)
77	1000Genomes_30x	NC_000002.12 - 215058191	Oct 12, 2022 (156)
78	The Avon Longitudinal Study of Parents and Children	NC_000002.11 - 215922915	Oct 11, 2018 (152)
79	Genetic variation in the Estonian population	NC_000002.11 - 215922915	Oct 11, 2018 (152)
80	The Danish reference pan genome	NC_000002.11 - 215922915	Apr 25, 2020 (154)
81	gnomAD - Genomes	NC_000002.12 - 215058191	Apr 26, 2021 (155)
82	Genome of the Netherlands Release 5	NC_000002.11 - 215922915	Apr 25, 2020 (154)
83	KOREAN population from KRGDB	NC_000002.11 - 215922915	Apr 25, 2020 (154)
84	Korean Genome Project	NC_000002.12 - 215058191	Apr 25, 2020 (154)
85	Northern Sweden	NC_000002.11 - 215922915	Jul 13, 2019 (153)
86	Qatari	NC_000002.11 - 215922915	Apr 25, 2020 (154)
87	SGDP_PRJ	NC_000002.11 - 215922915	Apr 25, 2020 (154)
88	Siberian	NC_000002.11 - 215922915	Apr 25, 2020 (154)
89	8.3KJPN	NC_000002.11 - 215922915	Apr 26, 2021 (155)
90	14KJPN	NC_000002.12 - 215058191	Oct 12, 2022 (156)
91	TopMed	NC_000002.12 - 215058191	Apr 26, 2021 (155)
92	UK 10K study - Twins	NC_000002.11 - 215922915	Oct 11, 2018 (152)
93	A Vietnamese Genetic Variation Database	NC_000002.11 - 215922915	Jul 13, 2019 (153)
94	ALFA	NC_000002.12 - 215058191	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)
rs61598806	May 27, 2008 (130)

Added to this RefSNP Cluster:

Submission IDs	Observation SPDI	Canonical SPDI	Source RSIDs
7463685, ss3900286291	NC_000002.11:215922914:A:C	NC_000002.12:215058190:A:C	(self)
7463685, ss3900286291	NC_000002.11:215922914:A:G	NC_000002.12:215058190:A:G	(self)
ss85859976	NC_000002.9:215748420:A:T	NC_000002.12:215058190:A:T	(self)
ss91541482, ss110740918, ss111635984, ss165459159, ss165895988, ss167568955, ss201722239, ss205844664, ss253868592, ss276893369, ss284539324, ss292485193, ss1587403269	NC_000002.10:215631159:A:T	NC_000002.12:215058190:A:T	(self)
12702210, 7022627, 4972346, 5483289, 3080971, 7463685, 2646587, 3234685, 6586257, 1722201, 14412414, 7022627, 1526862, ss219805579, ss231581842, ss239041556, ss556211160, ss649877941, ss977948362, ss1069931543, ss1301598776, ss1428907233, ss1579318350, ss1605767498, ss1648761531, ss1798335613, ss1921192755, ss1969021986, ss2021144246, ss2149205847, ss2625071496, ss2703854187, ss2786199505, ss2991338983, ss3344735725, ss3659234098, ss3729361722, ss3758068857, ss3784150992, ss3789689592, ss3794562769, ss3827500241, ss3837169656, ss3854569277, ss3900286291, ss5156443107, ss5335959831, ss5506794780, ss5630929798, ss5821575698, ss5957184190	NC_000002.11:215922914:A:T	NC_000002.12:215058190:A:T	(self)
16848095, 90589875, 6436981, 21147650, 348071440, 8146529284, ss2239053397, ss3024330220, ss3647271457, ss3705999082, ss3802432327, ss3842591372, ss3950058980, ss4544248561, ss5251992071, ss5451606364, ss5529322160, ss5687310546, ss5803211149, ss5852946615, ss5934658193	NC_000002.12:215058190:A:T	NC_000002.12:215058190:A:T	(self)
ss19411770, ss21571992	NT_005403.14:66132329:A:T	NC_000002.12:215058190:A:T	(self)
ss2202526, ss41823501, ss97120578, ss106159976, ss135973405, ss138627889	NT_005403.17:66132332:A:T	NC_000002.12:215058190:A: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 rs1403830

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

rs1403830