Name: rs228031
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.

rs228031

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr21:42648897 (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>T
Variation Type: SNV Single Nucleotide Variation
Frequency: A=0.258166 (68334/264690, TOPMED)
A=0.48039 (13575/28258, 14KJPN)
A=0.21986 (4253/19344, ALFA) (+ 15 more)
A=0.48162 (8072/16760, 8.3KJPN)
A=0.3073 (1968/6404, 1000G_30x)
A=0.3055 (1530/5008, 1000G)
A=0.1609 (721/4480, Estonian)
A=0.1876 (723/3854, ALSPAC)
A=0.1969 (730/3708, TWINSUK)
C=0.4993 (1463/2930, KOREAN)
A=0.4924 (902/1832, Korea1K)
A=0.147 (147/998, GoNL)
A=0.183 (110/600, NorthernSweden)
A=0.205 (96/468, SGDP_PRJ)
A=0.375 (81/216, Qatari)
A=0.452 (95/210, Vietnamese)
A=0.19 (10/54, Siberian)
A=0.15 (6/40, GENOME_DK)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: LOC101928255 : Non Coding Transcript 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	19344	A=0.21986	C=0.78014, T=0.00000
European	Sub	17378	A=0.19651	C=0.80349, T=0.00000
African	Sub	600	A=0.642	C=0.358, T=0.000
African Others	Sub	34	A=0.76	C=0.24, T=0.00
African American	Sub	566	A=0.634	C=0.366, T=0.000
Asian	Sub	50	A=0.82	C=0.18, T=0.00
East Asian	Sub	40	A=0.82	C=0.17, T=0.00
Other Asian	Sub	10	A=0.8	C=0.2, T=0.0
Latin American 1	Sub	28	A=0.61	C=0.39, T=0.00
Latin American 2	Sub	116	A=0.466	C=0.534, T=0.000
South Asian	Sub	24	A=0.25	C=0.75, T=0.00
Other	Sub	1148	A=0.2918	C=0.7082, T=0.0000

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=0.258166	C=0.741834
14KJPN	JAPANESE	Study-wide	28258	A=0.48039	C=0.51961
Allele Frequency Aggregator	Total	Global	19344	A=0.21986	C=0.78014, T=0.00000
Allele Frequency Aggregator	European	Sub	17378	A=0.19651	C=0.80349, T=0.00000
Allele Frequency Aggregator	Other	Sub	1148	A=0.2918	C=0.7082, T=0.0000
Allele Frequency Aggregator	African	Sub	600	A=0.642	C=0.358, T=0.000
Allele Frequency Aggregator	Latin American 2	Sub	116	A=0.466	C=0.534, T=0.000
Allele Frequency Aggregator	Asian	Sub	50	A=0.82	C=0.18, T=0.00
Allele Frequency Aggregator	Latin American 1	Sub	28	A=0.61	C=0.39, T=0.00
Allele Frequency Aggregator	South Asian	Sub	24	A=0.25	C=0.75, T=0.00
8.3KJPN	JAPANESE	Study-wide	16760	A=0.48162	C=0.51838
1000Genomes_30x	Global	Study-wide	6404	A=0.3073	C=0.6927
1000Genomes_30x	African	Sub	1786	A=0.3712	C=0.6288
1000Genomes_30x	Europe	Sub	1266	A=0.2141	C=0.7859
1000Genomes_30x	South Asian	Sub	1202	A=0.1930	C=0.8070
1000Genomes_30x	East Asian	Sub	1170	A=0.4957	C=0.5043
1000Genomes_30x	American	Sub	980	A=0.227	C=0.773
1000Genomes	Global	Study-wide	5008	A=0.3055	C=0.6945
1000Genomes	African	Sub	1322	A=0.3699	C=0.6301
1000Genomes	East Asian	Sub	1008	A=0.4891	C=0.5109
1000Genomes	Europe	Sub	1006	A=0.2097	C=0.7903
1000Genomes	South Asian	Sub	978	A=0.185	C=0.815
1000Genomes	American	Sub	694	A=0.225	C=0.775
Genetic variation in the Estonian population	Estonian	Study-wide	4480	A=0.1609	C=0.8391
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	A=0.1876	C=0.8124
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	A=0.1969	C=0.8031
KOREAN population from KRGDB	KOREAN	Study-wide	2930	A=0.5007	C=0.4993
Korean Genome Project	KOREAN	Study-wide	1832	A=0.4924	C=0.5076
Genome of the Netherlands Release 5	Genome of the Netherlands	Study-wide	998	A=0.147	C=0.853
Northern Sweden	ACPOP	Study-wide	600	A=0.183	C=0.817
SGDP_PRJ	Global	Study-wide	468	A=0.205	C=0.795
Qatari	Global	Study-wide	216	A=0.375	C=0.625
A Vietnamese Genetic Variation Database	Global	Study-wide	210	A=0.452	C=0.548
Siberian	Global	Study-wide	54	A=0.19	C=0.81
The Danish reference pan genome	Danish	Study-wide	40	A=0.15	C=0.85

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.42648897A>C
GRCh38.p14 chr 21	NC_000021.9:g.42648897A>T
GRCh37.p13 chr 21	NC_000021.8:g.44069007A>C
GRCh37.p13 chr 21	NC_000021.8:g.44069007A>T
PDE9A RefSeqGene	NG_047067.1:g.146A>C
PDE9A RefSeqGene	NG_047067.1:g.146A>T

Gene: LOC101928255, uncharacterized LOC101928255 (minus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
LOC101928255 transcript variant X1	XR_244322.4:n.3793T>G	N/A	Non Coding Transcript Variant
LOC101928255 transcript variant X1	XR_244322.4:n.3793T>A	N/A	Non Coding Transcript Variant
LOC101928255 transcript variant X2	XR_007067879.1:n.2971T>G	N/A	Non Coding Transcript Variant
LOC101928255 transcript variant X2	XR_007067879.1:n.2971T>A	N/A	Non Coding 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	A=	C	T
GRCh38.p14 chr 21	NC_000021.9:g.42648897=	NC_000021.9:g.42648897A>C	NC_000021.9:g.42648897A>T
GRCh37.p13 chr 21	NC_000021.8:g.44069007=	NC_000021.8:g.44069007A>C	NC_000021.8:g.44069007A>T
PDE9A RefSeqGene	NG_047067.1:g.146=	NG_047067.1:g.146A>C	NG_047067.1:g.146A>T
LOC101928255 transcript variant X1	XR_244322.4:n.3793=	XR_244322.4:n.3793T>G	XR_244322.4:n.3793T>A
LOC101928255 transcript variant X1	XR_244322.2:n.3577=	XR_244322.2:n.3577T>G	XR_244322.2:n.3577T>A
LOC101928255 transcript	XR_244322.1:n.2228=	XR_244322.1:n.2228T>G	XR_244322.1:n.2228T>A
LOC101928255 transcript variant X2	XR_007067879.1:n.2971=	XR_007067879.1:n.2971T>G	XR_007067879.1:n.2971T>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#.

89 SubSNP, 20 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	KWOK	ss295291	Jul 12, 2000 (79)
2	KWOK	ss1242703	Oct 04, 2000 (86)
3	KWOK	ss1839413	Oct 18, 2000 (87)
4	SC_JCM	ss2546300	Nov 08, 2000 (89)
5	BCM_SSAHASNP	ss10992926	Jul 11, 2003 (116)
6	SC_SNP	ss13445100	Dec 05, 2003 (119)
7	SSAHASNP	ss21835921	Apr 05, 2004 (121)
8	ABI	ss44290293	Mar 14, 2006 (126)
9	HGSV	ss78076031	Dec 06, 2007 (129)
10	HGSV	ss81878672	Dec 15, 2007 (130)
11	HUMANGENOME_JCVI	ss96150754	Feb 06, 2009 (130)
12	1000GENOMES	ss112507769	Jan 25, 2009 (130)
13	1000GENOMES	ss113953982	Jan 25, 2009 (130)
14	ILLUMINA-UK	ss117540949	Feb 14, 2009 (130)
15	CHURCH_CG54K	ss120034762	Dec 01, 2009 (131)
16	ENSEMBL	ss135594398	Dec 01, 2009 (131)
17	COMPLETE_GENOMICS	ss168120817	Jul 04, 2010 (132)
18	COMPLETE_GENOMICS	ss169625745	Jul 04, 2010 (132)
19	COMPLETE_GENOMICS	ss172078657	Jul 04, 2010 (132)
20	BUSHMAN	ss204030325	Jul 04, 2010 (132)
21	BCM-HGSC-SUB	ss208792524	Jul 04, 2010 (132)
22	1000GENOMES	ss228587851	Jul 14, 2010 (132)
23	1000GENOMES	ss237999347	Jul 15, 2010 (132)
24	1000GENOMES	ss244134319	Jul 15, 2010 (132)
25	BL	ss255992499	May 09, 2011 (134)
26	GMI	ss283557269	May 04, 2012 (137)
27	GMI	ss287538678	Apr 25, 2013 (138)
28	PJP	ss292718536	May 09, 2011 (134)
29	ILLUMINA	ss479350965	May 04, 2012 (137)
30	ILLUMINA	ss484278054	May 04, 2012 (137)
31	ILLUMINA	ss532916496	Sep 08, 2015 (146)
32	TISHKOFF	ss566523341	Apr 25, 2013 (138)
33	SSMP	ss662434128	Apr 25, 2013 (138)
34	ILLUMINA	ss779570535	Aug 21, 2014 (142)
35	ILLUMINA	ss780959817	Aug 21, 2014 (142)
36	ILLUMINA	ss835041853	Aug 21, 2014 (142)
37	EVA-GONL	ss995160493	Aug 21, 2014 (142)
38	JMKIDD_LAB	ss1082531742	Aug 21, 2014 (142)
39	1000GENOMES	ss1366442056	Aug 21, 2014 (142)
40	DDI	ss1429197447	Apr 01, 2015 (144)
41	EVA_GENOME_DK	ss1579680095	Apr 01, 2015 (144)
42	EVA_UK10K_ALSPAC	ss1639645637	Apr 01, 2015 (144)
43	EVA_UK10K_TWINSUK	ss1682639670	Apr 01, 2015 (144)
44	EVA_DECODE	ss1699232042	Apr 01, 2015 (144)
45	HAMMER_LAB	ss1809706774	Sep 08, 2015 (146)
46	WEILL_CORNELL_DGM	ss1938711192	Feb 12, 2016 (147)
47	GENOMED	ss1969235203	Jul 19, 2016 (147)
48	JJLAB	ss2030130194	Sep 14, 2016 (149)
49	USC_VALOUEV	ss2158735105	Dec 20, 2016 (150)
50	HUMAN_LONGEVITY	ss2246090164	Dec 20, 2016 (150)
51	SYSTEMSBIOZJU	ss2629564029	Nov 08, 2017 (151)
52	ILLUMINA	ss2633855184	Nov 08, 2017 (151)
53	GRF	ss2704466274	Nov 08, 2017 (151)
54	GNOMAD	ss2972214919	Nov 08, 2017 (151)
55	SWEGEN	ss3018955808	Nov 08, 2017 (151)
56	BIOINF_KMB_FNS_UNIBA	ss3028904864	Nov 08, 2017 (151)
57	CSHL	ss3352738902	Nov 08, 2017 (151)
58	ILLUMINA	ss3628491936	Oct 12, 2018 (152)
59	ILLUMINA	ss3631808413	Oct 12, 2018 (152)
60	ILLUMINA	ss3642207566	Oct 12, 2018 (152)
61	URBANLAB	ss3651124832	Oct 12, 2018 (152)
62	EGCUT_WGS	ss3685533338	Jul 13, 2019 (153)
63	EVA_DECODE	ss3707812216	Jul 13, 2019 (153)
64	ACPOP	ss3743768108	Jul 13, 2019 (153)
65	EVA	ss3759157378	Jul 13, 2019 (153)
66	PACBIO	ss3788775131	Jul 13, 2019 (153)
67	PACBIO	ss3793648065	Jul 13, 2019 (153)
68	PACBIO	ss3798534367	Jul 13, 2019 (153)
69	KHV_HUMAN_GENOMES	ss3822323542	Jul 13, 2019 (153)
70	EVA	ss3835896611	Apr 27, 2020 (154)
71	EVA	ss3841575863	Apr 27, 2020 (154)
72	EVA	ss3847089555	Apr 27, 2020 (154)
73	SGDP_PRJ	ss3890088160	Apr 27, 2020 (154)
74	KRGDB	ss3940433557	Apr 27, 2020 (154)
75	KOGIC	ss3983170721	Apr 27, 2020 (154)
76	TOPMED	ss5102908697	Apr 26, 2021 (155)
77	TOMMO_GENOMICS	ss5231702696	Apr 26, 2021 (155)
78	1000G_HIGH_COVERAGE	ss5310354170	Oct 16, 2022 (156)
79	EVA	ss5316042237	Oct 16, 2022 (156)
80	EVA	ss5440137748	Oct 16, 2022 (156)
81	HUGCELL_USP	ss5502390103	Oct 16, 2022 (156)
82	1000G_HIGH_COVERAGE	ss5617558730	Oct 16, 2022 (156)
83	SANFORD_IMAGENETICS	ss5664093648	Oct 16, 2022 (156)
84	TOMMO_GENOMICS	ss5792265065	Oct 16, 2022 (156)
85	YY_MCH	ss5818478530	Oct 16, 2022 (156)
86	EVA	ss5839096610	Oct 16, 2022 (156)
87	EVA	ss5853323340	Oct 16, 2022 (156)
88	EVA	ss5892515326	Oct 16, 2022 (156)
89	EVA	ss5958993124	Oct 16, 2022 (156)
90	1000Genomes	NC_000021.8 - 44069007	Oct 12, 2018 (152)
91	1000Genomes_30x	NC_000021.9 - 42648897	Oct 16, 2022 (156)
92	The Avon Longitudinal Study of Parents and Children	NC_000021.8 - 44069007	Oct 12, 2018 (152)
93	Genetic variation in the Estonian population	NC_000021.8 - 44069007	Oct 12, 2018 (152)
94	The Danish reference pan genome	NC_000021.8 - 44069007	Apr 27, 2020 (154)
95	gnomAD - Genomes Submission ignored due to conflicting rows: Row 564249657 (NC_000021.9:42648896:A:C 105962/139976) Row 564249658 (NC_000021.9:42648896:A:T 2/140030)	-	Apr 26, 2021 (155)
96	gnomAD - Genomes Submission ignored due to conflicting rows: Row 564249657 (NC_000021.9:42648896:A:C 105962/139976) Row 564249658 (NC_000021.9:42648896:A:T 2/140030)	-	Apr 26, 2021 (155)
97	Genome of the Netherlands Release 5	NC_000021.8 - 44069007	Apr 27, 2020 (154)
98	KOREAN population from KRGDB	NC_000021.8 - 44069007	Apr 27, 2020 (154)
99	Korean Genome Project	NC_000021.9 - 42648897	Apr 27, 2020 (154)
100	Northern Sweden	NC_000021.8 - 44069007	Jul 13, 2019 (153)
101	Qatari	NC_000021.8 - 44069007	Apr 27, 2020 (154)
102	SGDP_PRJ	NC_000021.8 - 44069007	Apr 27, 2020 (154)
103	Siberian	NC_000021.8 - 44069007	Apr 27, 2020 (154)
104	8.3KJPN	NC_000021.8 - 44069007	Apr 26, 2021 (155)
105	14KJPN	NC_000021.9 - 42648897	Oct 16, 2022 (156)
106	TopMed	NC_000021.9 - 42648897	Apr 26, 2021 (155)
107	UK 10K study - Twins	NC_000021.8 - 44069007	Oct 12, 2018 (152)
108	A Vietnamese Genetic Variation Database	NC_000021.8 - 44069007	Jul 13, 2019 (153)
109	ALFA	NC_000021.9 - 42648897	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)
rs60194890	May 25, 2008 (130)

Added to this RefSNP Cluster:

Submission IDs	Observation SPDI	Canonical SPDI	Source RSIDs
ss78076031, ss81878672, ss112507769, ss113953982, ss117540949, ss168120817, ss169625745, ss172078657, ss204030325, ss208792524, ss255992499, ss283557269, ss287538678, ss292718536, ss484278054, ss1699232042	NC_000021.7:42942075:A:C	NC_000021.9:42648896:A:C	(self)
79967729, 44261846, 31271586, 5845034, 19717156, 47610951, 17052973, 20753114, 42105140, 11251459, 89672003, 44261846, 9766642, ss228587851, ss237999347, ss244134319, ss479350965, ss532916496, ss566523341, ss662434128, ss779570535, ss780959817, ss835041853, ss995160493, ss1082531742, ss1366442056, ss1429197447, ss1579680095, ss1639645637, ss1682639670, ss1809706774, ss1938711192, ss1969235203, ss2030130194, ss2158735105, ss2629564029, ss2633855184, ss2704466274, ss2972214919, ss3018955808, ss3352738902, ss3628491936, ss3631808413, ss3642207566, ss3685533338, ss3743768108, ss3759157378, ss3788775131, ss3793648065, ss3798534367, ss3835896611, ss3841575863, ss3890088160, ss3940433557, ss5231702696, ss5316042237, ss5440137748, ss5664093648, ss5839096610, ss5958993124	NC_000021.8:44069006:A:C	NC_000021.9:42648896:A:C	(self)
105084665, 39548722, 126102169, 378017643, 720063563, ss2246090164, ss3028904864, ss3651124832, ss3707812216, ss3822323542, ss3847089555, ss3983170721, ss5102908697, ss5310354170, ss5502390103, ss5617558730, ss5792265065, ss5818478530, ss5853323340, ss5892515326	NC_000021.9:42648896:A:C	NC_000021.9:42648896:A:C	(self)
ss295291, ss1242703, ss1839413, ss2546300, ss44290293, ss96150754, ss120034762, ss135594398	NT_011515.12:1063447:A:C	NC_000021.9:42648896:A:C	(self)
ss10992926, ss13445100	NT_030188.2:818332:A:C	NC_000021.9:42648896:A:C	(self)
ss21835921	NT_030188.3:818332:A:C	NC_000021.9:42648896:A:C	(self)
720063563	NC_000021.9:42648896:A:T	NC_000021.9:42648896: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 rs228031

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

rs228031