Name: rs111952403
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.

rs111952403

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr21:38063648 (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>G / A>T
Variation Type: SNV Single Nucleotide Variation
Frequency: T=0.022944 (6073/264690, TOPMED)
T=0.04919 (1390/28258, 14KJPN)
T=0.01456 (275/18890, ALFA) (+ 12 more)
T=0.05030 (843/16760, 8.3KJPN)
T=0.0320 (205/6404, 1000G_30x)
T=0.0347 (174/5008, 1000G)
T=0.0092 (41/4480, Estonian)
T=0.0101 (39/3854, ALSPAC)
T=0.0102 (38/3708, TWINSUK)
T=0.0595 (109/1832, Korea1K)
T=0.007 (7/998, GoNL)
T=0.003 (2/600, NorthernSweden)
T=0.005 (1/216, Qatari)
T=0.125 (27/216, Vietnamese)
A=0.43 (13/30, SGDP_PRJ)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: DSCR4 : 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=0.98544	T=0.01456
European	Sub	14286	A=0.99076	T=0.00924
African	Sub	2946	A=0.9616	T=0.0384
African Others	Sub	114	A=0.956	T=0.044
African American	Sub	2832	A=0.9619	T=0.0381
Asian	Sub	112	A=0.920	T=0.080
East Asian	Sub	86	A=0.93	T=0.07
Other Asian	Sub	26	A=0.88	T=0.12
Latin American 1	Sub	146	A=0.986	T=0.014
Latin American 2	Sub	610	A=0.993	T=0.007
South Asian	Sub	98	A=1.00	T=0.00
Other	Sub	692	A=0.978	T=0.022

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=0.977056	T=0.022944
14KJPN	JAPANESE	Study-wide	28258	A=0.95081	T=0.04919
Allele Frequency Aggregator	Total	Global	18890	A=0.98544	T=0.01456
Allele Frequency Aggregator	European	Sub	14286	A=0.99076	T=0.00924
Allele Frequency Aggregator	African	Sub	2946	A=0.9616	T=0.0384
Allele Frequency Aggregator	Other	Sub	692	A=0.978	T=0.022
Allele Frequency Aggregator	Latin American 2	Sub	610	A=0.993	T=0.007
Allele Frequency Aggregator	Latin American 1	Sub	146	A=0.986	T=0.014
Allele Frequency Aggregator	Asian	Sub	112	A=0.920	T=0.080
Allele Frequency Aggregator	South Asian	Sub	98	A=1.00	T=0.00
8.3KJPN	JAPANESE	Study-wide	16760	A=0.94970	T=0.05030
1000Genomes_30x	Global	Study-wide	6404	A=0.9680	T=0.0320
1000Genomes_30x	African	Sub	1786	A=0.9580	T=0.0420
1000Genomes_30x	Europe	Sub	1266	A=0.9905	T=0.0095
1000Genomes_30x	South Asian	Sub	1202	A=0.9967	T=0.0033
1000Genomes_30x	East Asian	Sub	1170	A=0.9077	T=0.0923
1000Genomes_30x	American	Sub	980	A=0.994	T=0.006
1000Genomes	Global	Study-wide	5008	A=0.9653	T=0.0347
1000Genomes	African	Sub	1322	A=0.9523	T=0.0477
1000Genomes	East Asian	Sub	1008	A=0.9077	T=0.0923
1000Genomes	Europe	Sub	1006	A=0.9891	T=0.0109
1000Genomes	South Asian	Sub	978	A=0.996	T=0.004
1000Genomes	American	Sub	694	A=0.996	T=0.004
Genetic variation in the Estonian population	Estonian	Study-wide	4480	A=0.9908	T=0.0092
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	A=0.9899	T=0.0101
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	A=0.9898	T=0.0102
Korean Genome Project	KOREAN	Study-wide	1832	A=0.9405	T=0.0595
Genome of the Netherlands Release 5	Genome of the Netherlands	Study-wide	998	A=0.993	T=0.007
Northern Sweden	ACPOP	Study-wide	600	A=0.997	T=0.003
Qatari	Global	Study-wide	216	A=0.995	T=0.005
A Vietnamese Genetic Variation Database	Global	Study-wide	216	A=0.875	T=0.125
SGDP_PRJ	Global	Study-wide	30	A=0.43	T=0.57

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.38063648A>G
GRCh38.p14 chr 21	NC_000021.9:g.38063648A>T
GRCh37.p13 chr 21	NC_000021.8:g.39435950A>G
GRCh37.p13 chr 21	NC_000021.8:g.39435950A>T

Gene: DSCR4, Down syndrome critical region 4 (minus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
DSCR4 transcript	NR_147130.1:n.	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=	G	T
GRCh38.p14 chr 21	NC_000021.9:g.38063648=	NC_000021.9:g.38063648A>G	NC_000021.9:g.38063648A>T
GRCh37.p13 chr 21	NC_000021.8:g.39435950=	NC_000021.8:g.39435950A>G	NC_000021.8:g.39435950A>T
DSCR4 transcript	NM_005867.2:c.231-8875=	NM_005867.2:c.231-8875T>C	NM_005867.2:c.231-8875T>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#.

39 SubSNP, 17 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	BUSHMAN	ss204016962	Jul 04, 2010 (132)
2	1000GENOMES	ss228564058	Jul 14, 2010 (132)
3	1000GENOMES	ss244120704	Jul 15, 2010 (132)
4	GMI	ss283541697	May 04, 2012 (137)
5	TISHKOFF	ss566495815	Apr 25, 2013 (138)
6	SSMP	ss662406286	Apr 25, 2013 (138)
7	EVA-GONL	ss995120189	Aug 21, 2014 (142)
8	JMKIDD_LAB	ss1082500482	Aug 21, 2014 (142)
9	1000GENOMES	ss1366297658	Aug 21, 2014 (142)
10	EVA_UK10K_ALSPAC	ss1639566024	Apr 01, 2015 (144)
11	EVA_UK10K_TWINSUK	ss1682560057	Apr 01, 2015 (144)
12	EVA_DECODE	ss1699190584	Apr 01, 2015 (144)
13	HAMMER_LAB	ss1809687071	Sep 08, 2015 (146)
14	WEILL_CORNELL_DGM	ss1938670245	Feb 12, 2016 (147)
15	HUMAN_LONGEVITY	ss2245794914	Dec 20, 2016 (150)
16	GRF	ss2704442682	Nov 08, 2017 (151)
17	GNOMAD	ss2971826864	Nov 08, 2017 (151)
18	SWEGEN	ss3018895912	Nov 08, 2017 (151)
19	EGCUT_WGS	ss3685472846	Jul 13, 2019 (153)
20	EVA_DECODE	ss3707736013	Jul 13, 2019 (153)
21	ACPOP	ss3743733914	Jul 13, 2019 (153)
22	EVA	ss3759110039	Jul 13, 2019 (153)
23	KHV_HUMAN_GENOMES	ss3822276292	Jul 13, 2019 (153)
24	SGDP_PRJ	ss3890006603	Apr 27, 2020 (154)
25	KOGIC	ss3983100564	Apr 27, 2020 (154)
26	TOPMED	ss5101719042	Apr 26, 2021 (155)
27	TOMMO_GENOMICS	ss5231544479	Apr 26, 2021 (155)
28	1000G_HIGH_COVERAGE	ss5310227399	Oct 13, 2022 (156)
29	EVA	ss5439905513	Oct 13, 2022 (156)
30	HUGCELL_USP	ss5502273975	Oct 13, 2022 (156)
31	EVA	ss5512324169	Oct 13, 2022 (156)
32	1000G_HIGH_COVERAGE	ss5617374807	Oct 13, 2022 (156)
33	SANFORD_IMAGENETICS	ss5664019114	Oct 13, 2022 (156)
34	TOMMO_GENOMICS	ss5792060882	Oct 13, 2022 (156)
35	YY_MCH	ss5818445999	Oct 13, 2022 (156)
36	EVA	ss5839044297	Oct 13, 2022 (156)
37	EVA	ss5853305902	Oct 13, 2022 (156)
38	EVA	ss5892366885	Oct 13, 2022 (156)
39	EVA	ss5958914869	Oct 13, 2022 (156)
40	1000Genomes	NC_000021.8 - 39435950	Oct 12, 2018 (152)
41	1000Genomes_30x	NC_000021.9 - 38063648	Oct 13, 2022 (156)
42	The Avon Longitudinal Study of Parents and Children	NC_000021.8 - 39435950	Oct 12, 2018 (152)
43	Genetic variation in the Estonian population	NC_000021.8 - 39435950	Oct 12, 2018 (152)
44	gnomAD - Genomes Submission ignored due to conflicting rows: Row 563274411 (NC_000021.9:38063647:A:G 1/140186) Row 563274412 (NC_000021.9:38063647:A:T 2986/140178)	-	Apr 26, 2021 (155)
45	gnomAD - Genomes Submission ignored due to conflicting rows: Row 563274411 (NC_000021.9:38063647:A:G 1/140186) Row 563274412 (NC_000021.9:38063647:A:T 2986/140178)	-	Apr 26, 2021 (155)
46	Genome of the Netherlands Release 5	NC_000021.8 - 39435950	Apr 27, 2020 (154)
47	Korean Genome Project	NC_000021.9 - 38063648	Apr 27, 2020 (154)
48	Northern Sweden	NC_000021.8 - 39435950	Jul 13, 2019 (153)
49	Qatari	NC_000021.8 - 39435950	Apr 27, 2020 (154)
50	SGDP_PRJ	NC_000021.8 - 39435950	Apr 27, 2020 (154)
51	8.3KJPN	NC_000021.8 - 39435950	Apr 26, 2021 (155)
52	14KJPN	NC_000021.9 - 38063648	Oct 13, 2022 (156)
53	TopMed	NC_000021.9 - 38063648	Apr 26, 2021 (155)
54	UK 10K study - Twins	NC_000021.8 - 39435950	Oct 12, 2018 (152)
55	A Vietnamese Genetic Variation Database	NC_000021.8 - 39435950	Jul 13, 2019 (153)
56	ALFA	NC_000021.9 - 38063648	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
	NC_000021.9:38063647:A:G	NC_000021.9:38063647:A:G	(self)
ss204016962, ss283541697, ss1699190584	NC_000021.7:38357819:A:T	NC_000021.9:38063647:A:T	(self)
79817914, 44174178, 31211094, 19677958, 17018779, 20712167, 42023583, 89513786, 44174178, 9746475, ss228564058, ss244120704, ss566495815, ss662406286, ss995120189, ss1082500482, ss1366297658, ss1639566024, ss1682560057, ss1809687071, ss1938670245, ss2704442682, ss2971826864, ss3018895912, ss3685472846, ss3743733914, ss3759110039, ss3890006603, ss5231544479, ss5439905513, ss5512324169, ss5664019114, ss5839044297, ss5958914869	NC_000021.8:39435949:A:T	NC_000021.9:38063647:A:T	(self)
104900742, 39478565, 125897986, 376827988, 4276210950, ss2245794914, ss3707736013, ss3822276292, ss3983100564, ss5101719042, ss5310227399, ss5502273975, ss5617374807, ss5792060882, ss5818445999, ss5853305902, ss5892366885	NC_000021.9:38063647:A:T	NC_000021.9:38063647: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 rs111952403

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

rs111952403