Name: rs3214074
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.

rs3214074

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr21:44287633 (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: delA
Variation Type: Deletion
Frequency: delA=0.080751 (21374/264690, TOPMED)
delA=0.053180 (8049/151354, GnomAD_exome)
delA=0.069776 (9778/140134, GnomAD) (+ 12 more)
delA=0.30671 (8667/28258, 14KJPN)
delA=0.00794 (209/26316, ALFA)
delA=0.05086 (906/17814, ExAC)
delA=0.30817 (5165/16760, 8.3KJPN)
delA=0.06371 (744/11678, GO-ESP)
delA=0.1351 (865/6404, 1000G_30x)
delA=0.0100 (45/4480, Estonian)
delA=0.0005 (2/3854, ALSPAC)
delA=0.0011 (4/3708, TWINSUK)
delA=0.4023 (737/1832, Korea1K)
delA=0.007 (4/600, NorthernSweden)
delA=0.341 (73/214, Vietnamese)

Clinical Significance: Reported in ClinVar
Gene : Consequence: AIRE : 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: 20231103111315

Population	Group	Sample Size	Ref Allele	Alt Allele	Ref HMOZ	Alt HMOZ	HTRZ	HWEP
Total	Global	26316	A=0.99206	=0.00794	0.984876	0.00076	0.014364	32
European	Sub	20176	A=0.99485	=0.00515	0.990087	0.000397	0.009516	28
African	Sub	2534	A=0.9799	=0.0201	0.962115	0.002368	0.035517	7
African Others	Sub	66	A=0.97	=0.03	0.939394	0.0	0.060606	0
African American	Sub	2468	A=0.9801	=0.0199	0.962723	0.002431	0.034846	8
Asian	Sub	118	A=0.864	=0.136	0.762712	0.033898	0.20339	1
East Asian	Sub	68	A=0.85	=0.15	0.735294	0.029412	0.235294	0
Other Asian	Sub	50	A=0.88	=0.12	0.8	0.04	0.16	1
Latin American 1	Sub	132	A=1.000	=0.000	1.0	0.0	0.0	N/A
Latin American 2	Sub	552	A=1.000	=0.000	1.0	0.0	0.0	N/A
South Asian	Sub	94	A=1.00	=0.00	1.0	0.0	0.0	N/A
Other	Sub	2710	A=0.9860	=0.0140	0.972694	0.000738	0.026568	1

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=0.919249	delA=0.080751
gnomAD - Exomes	Global	Study-wide	151354	A=0.946820	delA=0.053180
gnomAD - Exomes	European	Sub	71888	A=0.99574	delA=0.00426
gnomAD - Exomes	Asian	Sub	34156	A=0.86404	delA=0.13596
gnomAD - Exomes	American	Sub	24698	A=0.94433	delA=0.05567
gnomAD - Exomes	Ashkenazi Jewish	Sub	8418	A=0.9846	delA=0.0154
gnomAD - Exomes	African	Sub	7854	A=0.8122	delA=0.1878
gnomAD - Exomes	Other	Sub	4340	A=0.9726	delA=0.0274
gnomAD - Genomes	Global	Study-wide	140134	A=0.930224	delA=0.069776
gnomAD - Genomes	European	Sub	75920	A=0.99675	delA=0.00325
gnomAD - Genomes	African	Sub	41958	A=0.81751	delA=0.18249
gnomAD - Genomes	American	Sub	13664	A=0.95887	delA=0.04113
gnomAD - Genomes	Ashkenazi Jewish	Sub	3320	A=0.9834	delA=0.0166
gnomAD - Genomes	East Asian	Sub	3120	A=0.6426	delA=0.3574
gnomAD - Genomes	Other	Sub	2152	A=0.9340	delA=0.0660
14KJPN	JAPANESE	Study-wide	28258	A=0.69329	delA=0.30671
Allele Frequency Aggregator	Total	Global	26316	A=0.99206	delA=0.00794
Allele Frequency Aggregator	European	Sub	20176	A=0.99485	delA=0.00515
Allele Frequency Aggregator	Other	Sub	2710	A=0.9860	delA=0.0140
Allele Frequency Aggregator	African	Sub	2534	A=0.9799	delA=0.0201
Allele Frequency Aggregator	Latin American 2	Sub	552	A=1.000	delA=0.000
Allele Frequency Aggregator	Latin American 1	Sub	132	A=1.000	delA=0.000
Allele Frequency Aggregator	Asian	Sub	118	A=0.864	delA=0.136
Allele Frequency Aggregator	South Asian	Sub	94	A=1.00	delA=0.00
ExAC	Global	Study-wide	17814	A=0.94914	delA=0.05086
ExAC	Asian	Sub	8590	A=0.9497	delA=0.0503
ExAC	Europe	Sub	6706	A=0.9928	delA=0.0072
ExAC	African	Sub	1962	A=0.7982	delA=0.2018
ExAC	American	Sub	384	A=0.948	delA=0.052
ExAC	Other	Sub	172	A=0.942	delA=0.058
8.3KJPN	JAPANESE	Study-wide	16760	A=0.69183	delA=0.30817
GO Exome Sequencing Project	Global	Study-wide	11678	A=0.93629	delA=0.06371
GO Exome Sequencing Project	European American	Sub	7736	A=0.9969	delA=0.0031
GO Exome Sequencing Project	African American	Sub	3942	A=0.8174	delA=0.1826
1000Genomes_30x	Global	Study-wide	6404	A=0.8649	delA=0.1351
1000Genomes_30x	African	Sub	1786	A=0.8012	delA=0.1988
1000Genomes_30x	Europe	Sub	1266	A=0.9961	delA=0.0039
1000Genomes_30x	South Asian	Sub	1202	A=0.9750	delA=0.0250
1000Genomes_30x	East Asian	Sub	1170	A=0.6521	delA=0.3479
1000Genomes_30x	American	Sub	980	A=0.931	delA=0.069
Genetic variation in the Estonian population	Estonian	Study-wide	4480	A=0.9900	delA=0.0100
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	A=0.9995	delA=0.0005
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	A=0.9989	delA=0.0011
Korean Genome Project	KOREAN	Study-wide	1832	A=0.5977	delA=0.4023
Northern Sweden	ACPOP	Study-wide	600	A=0.993	delA=0.007
A Vietnamese Genetic Variation Database	Global	Study-wide	214	A=0.659	delA=0.341

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 21	NC_000021.9:g.44287633del
GRCh37.p13 chr 21	NC_000021.8:g.45707516del
AIRE RefSeqGene (LRG_18)	NG_009556.1:g.6754del

Gene: AIRE, autoimmune regulator (plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
AIRE transcript	NM_000383.4:c.538+42del	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.

Allele: delA (allele ID: 44331 )

ClinVar Accession	Disease Names	Clinical Significance
RCV001778669.2	not specified	Benign

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=	delA
GRCh38.p14 chr 21	NC_000021.9:g.44287633=	NC_000021.9:g.44287633del
GRCh37.p13 chr 21	NC_000021.8:g.45707516=	NC_000021.8:g.45707516del
AIRE RefSeqGene (LRG_18)	NG_009556.1:g.6754=	NG_009556.1:g.6754del
AIRE transcript	NM_000383.3:c.538+42=	NM_000383.3:c.538+42del
AIRE transcript	NM_000383.4:c.538+42=	NM_000383.4:c.538+42del

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#.

47 SubSNP, 15 Frequency, 1 ClinVar submissions

No	Submitter	Submission ID	Date (Build)
1	YUSUKE	ss4475008	Jul 03, 2002 (106)
2	CGM_KYOTO	ss76864781	Dec 07, 2007 (129)
3	HGSV	ss81095454	Dec 15, 2007 (130)
4	GMI	ss155832090	Dec 01, 2009 (131)
5	BUSHMAN	ss193637381	Jul 04, 2010 (132)
6	GMI	ss289438151	May 04, 2012 (137)
7	1000GENOMES	ss327993277	May 09, 2011 (136)
8	1000GENOMES	ss328319990	May 09, 2011 (136)
9	CORRELAGEN	ss475578797	Nov 22, 2011 (136)
10	1000GENOMES	ss499822758	May 04, 2012 (137)
11	LUNTER	ss553125402	Apr 25, 2013 (138)
12	LUNTER	ss553697455	Apr 25, 2013 (138)
13	TISHKOFF	ss555023581	Apr 25, 2013 (138)
14	SSMP	ss664511628	Apr 01, 2015 (144)
15	EVA_DECODE	ss1699246146	Apr 01, 2015 (144)
16	EVA_UK10K_ALSPAC	ss1709525574	Apr 01, 2015 (144)
17	EVA_UK10K_TWINSUK	ss1709525654	Apr 01, 2015 (144)
18	EVA_EXAC	ss1712240670	Apr 01, 2015 (144)
19	HAMMER_LAB	ss1809713403	Sep 08, 2015 (146)
20	JJLAB	ss2031458296	Sep 14, 2016 (149)
21	SYSTEMSBIOZJU	ss2629567925	Nov 08, 2017 (151)
22	GNOMAD	ss2744886264	Nov 08, 2017 (151)
23	GNOMAD	ss2750472373	Nov 08, 2017 (151)
24	GNOMAD	ss2972363759	Nov 08, 2017 (151)
25	SWEGEN	ss3018978149	Nov 08, 2017 (151)
26	MCHAISSO	ss3064018723	Nov 08, 2017 (151)
27	MCHAISSO	ss3065844631	Nov 08, 2017 (151)
28	EGCUT_WGS	ss3685554249	Jul 13, 2019 (153)
29	EVA_DECODE	ss3707833089	Jul 13, 2019 (153)
30	ACPOP	ss3743779906	Jul 13, 2019 (153)
31	KHV_HUMAN_GENOMES	ss3822338713	Jul 13, 2019 (153)
32	EVA	ss3825412581	Apr 27, 2020 (154)
33	KOGIC	ss3983192626	Apr 27, 2020 (154)
34	EVA	ss3986848491	Apr 26, 2021 (155)
35	TOPMED	ss5103212524	Apr 26, 2021 (155)
36	TOMMO_GENOMICS	ss5231765507	Apr 26, 2021 (155)
37	1000G_HIGH_COVERAGE	ss5310389092	Oct 16, 2022 (156)
38	HUGCELL_USP	ss5502419150	Oct 16, 2022 (156)
39	1000G_HIGH_COVERAGE	ss5617609770	Oct 16, 2022 (156)
40	SANFORD_IMAGENETICS	ss5664120297	Oct 16, 2022 (156)
41	TOMMO_GENOMICS	ss5792331477	Oct 16, 2022 (156)
42	YY_MCH	ss5818487439	Oct 16, 2022 (156)
43	EVA	ss5839116040	Oct 16, 2022 (156)
44	EVA	ss5848559518	Oct 16, 2022 (156)
45	EVA	ss5853327205	Oct 16, 2022 (156)
46	EVA	ss5892552787	Oct 16, 2022 (156)
47	EVA	ss5959020072	Oct 16, 2022 (156)
48	1000Genomes_30x	NC_000021.9 - 44287633	Oct 16, 2022 (156)
49	The Avon Longitudinal Study of Parents and Children	NC_000021.8 - 45707516	Oct 12, 2018 (152)
50	Genetic variation in the Estonian population	NC_000021.8 - 45707516	Oct 12, 2018 (152)
51	ExAC	NC_000021.8 - 45707516	Oct 12, 2018 (152)
52	gnomAD - Genomes	NC_000021.9 - 44287633	Apr 26, 2021 (155)
53	gnomAD - Exomes	NC_000021.8 - 45707516	Jul 13, 2019 (153)
54	GO Exome Sequencing Project	NC_000021.8 - 45707516	Oct 12, 2018 (152)
55	Korean Genome Project	NC_000021.9 - 44287633	Apr 27, 2020 (154)
56	Northern Sweden	NC_000021.8 - 45707516	Jul 13, 2019 (153)
57	8.3KJPN	NC_000021.8 - 45707516	Apr 26, 2021 (155)
58	14KJPN	NC_000021.9 - 44287633	Oct 16, 2022 (156)
59	TopMed	NC_000021.9 - 44287633	Apr 26, 2021 (155)
60	UK 10K study - Twins	NC_000021.8 - 45707516	Oct 12, 2018 (152)
61	A Vietnamese Genetic Variation Database	NC_000021.8 - 45707516	Jul 13, 2019 (153)
62	ALFA	NC_000021.9 - 44287633	Apr 26, 2021 (155)
63	ClinVar	RCV001778669.2	Oct 16, 2022 (156)

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)
rs59584004	May 25, 2008 (130)
rs142025373	Nov 21, 2011 (136)

Added to this RefSNP Cluster:

Submission IDs	Observation SPDI	Canonical SPDI	Source RSIDs
ss81095454, ss289438151, ss327993277, ss328319990, ss553125402, ss553697455, ss1699246146	NC_000021.7:44531943:A:	NC_000021.9:44287632:A:	(self)
44291669, 31292497, 5747773, 14213782, 1869449, 17064771, 89734814, 44291669, 9772250, ss499822758, ss555023581, ss664511628, ss1709525574, ss1709525654, ss1712240670, ss1809713403, ss2031458296, ss2629567925, ss2744886264, ss2750472373, ss2972363759, ss3018978149, ss3685554249, ss3743779906, ss3825412581, ss3986848491, ss5231765507, ss5664120297, ss5839116040, ss5848559518, ss5959020072	NC_000021.8:45707515:A:	NC_000021.9:44287632:A:	(self)
RCV001778669.2, 105135705, 564517600, 39570627, 126168581, 378321470, 4564444433, ss475578797, ss3064018723, ss3065844631, ss3707833089, ss3822338713, ss3983192626, ss5103212524, ss5310389092, ss5502419150, ss5617609770, ss5792331477, ss5818487439, ss5853327205, ss5892552787	NC_000021.9:44287632:A:	NC_000021.9:44287632:A:	(self)
ss193637381	NT_011512.12:31321824:A:	NC_000021.9:44287632:A:	(self)
ss4475008, ss76864781, ss155832090	NT_011515.12:2701956:A:	NC_000021.9:44287632: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 rs3214074

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

rs3214074