Name: rs9754270
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.

rs9754270

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr21:40709594 (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: C>A / C>G
Variation Type: SNV Single Nucleotide Variation
Frequency: G=0.324183 (85808/264690, TOPMED)
G=0.30505 (8620/28258, 14KJPN)
G=0.30561 (5122/16760, 8.3KJPN) (+ 11 more)
G=0.12048 (1534/12732, ALFA)
G=0.3278 (2099/6404, 1000G_30x)
G=0.3239 (1622/5008, 1000G)
G=0.2196 (982/4472, Estonian)
G=0.3010 (882/2930, KOREAN)
G=0.3422 (627/1832, Korea1K)
G=0.239 (239/998, GoNL)
C=0.358 (113/316, SGDP_PRJ)
G=0.301 (65/216, Qatari)
G=0.316 (67/212, Vietnamese)
C=0.33 (6/18, Siberian)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: DSCAM : 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	12732	C=0.87920	A=0.00031, G=0.12048
European	Sub	10918	C=0.86325	A=0.00037, G=0.13638
African	Sub	956	C=0.962	A=0.000, G=0.038
African Others	Sub	32	C=0.88	A=0.00, G=0.12
African American	Sub	924	C=0.965	A=0.000, G=0.035
Asian	Sub	56	C=0.98	A=0.00, G=0.02
East Asian	Sub	44	C=1.00	A=0.00, G=0.00
Other Asian	Sub	12	C=0.92	A=0.00, G=0.08
Latin American 1	Sub	74	C=1.00	A=0.00, G=0.00
Latin American 2	Sub	310	C=1.000	A=0.000, G=0.000
South Asian	Sub	66	C=0.98	A=0.00, G=0.02
Other	Sub	352	C=0.980	A=0.000, G=0.020

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	C=0.675817	G=0.324183
14KJPN	JAPANESE	Study-wide	28258	C=0.69495	G=0.30505
8.3KJPN	JAPANESE	Study-wide	16760	C=0.69439	G=0.30561
Allele Frequency Aggregator	Total	Global	12732	C=0.87920	A=0.00031, G=0.12048
Allele Frequency Aggregator	European	Sub	10918	C=0.86325	A=0.00037, G=0.13638
Allele Frequency Aggregator	African	Sub	956	C=0.962	A=0.000, G=0.038
Allele Frequency Aggregator	Other	Sub	352	C=0.980	A=0.000, G=0.020
Allele Frequency Aggregator	Latin American 2	Sub	310	C=1.000	A=0.000, G=0.000
Allele Frequency Aggregator	Latin American 1	Sub	74	C=1.00	A=0.00, G=0.00
Allele Frequency Aggregator	South Asian	Sub	66	C=0.98	A=0.00, G=0.02
Allele Frequency Aggregator	Asian	Sub	56	C=0.98	A=0.00, G=0.02
1000Genomes_30x	Global	Study-wide	6404	C=0.6722	G=0.3278
1000Genomes_30x	African	Sub	1786	C=0.5638	G=0.4362
1000Genomes_30x	Europe	Sub	1266	C=0.7401	G=0.2599
1000Genomes_30x	South Asian	Sub	1202	C=0.7446	G=0.2554
1000Genomes_30x	East Asian	Sub	1170	C=0.6855	G=0.3145
1000Genomes_30x	American	Sub	980	C=0.678	G=0.322
1000Genomes	Global	Study-wide	5008	C=0.6761	G=0.3239
1000Genomes	African	Sub	1322	C=0.5703	G=0.4297
1000Genomes	East Asian	Sub	1008	C=0.6905	G=0.3095
1000Genomes	Europe	Sub	1006	C=0.7276	G=0.2724
1000Genomes	South Asian	Sub	978	C=0.758	G=0.242
1000Genomes	American	Sub	694	C=0.667	G=0.333
Genetic variation in the Estonian population	Estonian	Study-wide	4472	C=0.7804	G=0.2196
KOREAN population from KRGDB	KOREAN	Study-wide	2930	C=0.6990	G=0.3010
Korean Genome Project	KOREAN	Study-wide	1832	C=0.6578	G=0.3422
Genome of the Netherlands Release 5	Genome of the Netherlands	Study-wide	998	C=0.761	G=0.239
SGDP_PRJ	Global	Study-wide	316	C=0.358	G=0.642
Qatari	Global	Study-wide	216	C=0.699	G=0.301
A Vietnamese Genetic Variation Database	Global	Study-wide	212	C=0.684	G=0.316
Siberian	Global	Study-wide	18	C=0.33	G=0.67

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.40709594C>A
GRCh38.p14 chr 21	NC_000021.9:g.40709594C>G
GRCh37.p13 chr 21	NC_000021.8:g.42081520C>A
GRCh37.p13 chr 21	NC_000021.8:g.42081520C>G
GRCh38.p14 chr 21 fix patch HG2265_PATCH	NW_025791814.1:g.849248C>A
GRCh38.p14 chr 21 fix patch HG2265_PATCH	NW_025791814.1:g.849248C>G

Gene: DSCAM, DS cell adhesion molecule (minus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
DSCAM transcript variant 2	NM_001271534.3:c.44-823G>T	N/A	Intron Variant
DSCAM transcript variant 1	NM_001389.5:c.44-823G>T	N/A	Intron Variant
DSCAM transcript variant 3	NR_073202.3:n.	N/A	Intron Variant
DSCAM transcript variant X1	XM_017028281.2:c.	N/A	Genic Upstream 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	C=	A	G
GRCh38.p14 chr 21	NC_000021.9:g.40709594=	NC_000021.9:g.40709594C>A	NC_000021.9:g.40709594C>G
GRCh37.p13 chr 21	NC_000021.8:g.42081520=	NC_000021.8:g.42081520C>A	NC_000021.8:g.42081520C>G
GRCh38.p14 chr 21 fix patch HG2265_PATCH	NW_025791814.1:g.849248=	NW_025791814.1:g.849248C>A	NW_025791814.1:g.849248C>G
DSCAM transcript variant 2	NM_001271534.1:c.44-823=	NM_001271534.1:c.44-823G>T	NM_001271534.1:c.44-823G>C
DSCAM transcript variant 2	NM_001271534.3:c.44-823=	NM_001271534.3:c.44-823G>T	NM_001271534.3:c.44-823G>C
DSCAM transcript variant 1	NM_001389.3:c.44-823=	NM_001389.3:c.44-823G>T	NM_001389.3:c.44-823G>C
DSCAM transcript variant 1	NM_001389.5:c.44-823=	NM_001389.5:c.44-823G>T	NM_001389.5:c.44-823G>C

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#.

54 SubSNP, 22 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	BCM_SSAHASNP	ss13569608	Dec 05, 2003 (119)
2	SSAHASNP	ss21832488	Apr 05, 2004 (123)
3	HGSV	ss78857443	Dec 06, 2007 (129)
4	BCMHGSC_JDW	ss91845877	Mar 24, 2008 (129)
5	ENSEMBL	ss133097995	Dec 01, 2009 (131)
6	ENSEMBL	ss138320573	Dec 01, 2009 (131)
7	BUSHMAN	ss204024032	Jul 04, 2010 (142)
8	GMI	ss283550851	May 04, 2012 (137)
9	PJP	ss292715111	May 09, 2011 (134)
10	1000GENOMES	ss341032299	May 09, 2011 (134)
11	SSMP	ss662421655	Apr 25, 2013 (138)
12	EVA-GONL	ss995142274	Aug 21, 2014 (142)
13	JMKIDD_LAB	ss1082518015	Aug 21, 2014 (142)
14	1000GENOMES	ss1366378022	Aug 21, 2014 (142)
15	DDI	ss1429191642	Apr 01, 2015 (144)
16	EVA_UK10K_ALSPAC	ss1639610598	Apr 01, 2015 (144)
17	EVA_UK10K_ALSPAC	ss1639610599	Apr 01, 2015 (144)
18	EVA_UK10K_TWINSUK	ss1682604631	Apr 01, 2015 (144)
19	EVA_UK10K_TWINSUK	ss1682604632	Apr 01, 2015 (144)
20	HAMMER_LAB	ss1809698231	Sep 08, 2015 (146)
21	WEILL_CORNELL_DGM	ss1938692543	Feb 12, 2016 (147)
22	JJLAB	ss2030119534	Sep 14, 2016 (149)
23	USC_VALOUEV	ss2158724504	Dec 20, 2016 (150)
24	HUMAN_LONGEVITY	ss2245959866	Dec 20, 2016 (150)
25	SYSTEMSBIOZJU	ss2629559398	Nov 08, 2017 (151)
26	GRF	ss2704456147	Nov 08, 2017 (151)
27	GNOMAD	ss2972045776	Nov 08, 2017 (151)
28	SWEGEN	ss3018929622	Nov 08, 2017 (151)
29	CSHL	ss3352729906	Nov 08, 2017 (151)
30	URBANLAB	ss3651120954	Oct 12, 2018 (152)
31	EGCUT_WGS	ss3685506947	Jul 13, 2019 (153)
32	EVA_DECODE	ss3707778540	Jul 13, 2019 (153)
33	EVA_DECODE	ss3707778541	Jul 13, 2019 (153)
34	ACPOP	ss3743752939	Jul 13, 2019 (153)
35	ACPOP	ss3743752940	Jul 13, 2019 (153)
36	EVA	ss3759135981	Jul 13, 2019 (153)
37	KHV_HUMAN_GENOMES	ss3822303007	Jul 13, 2019 (153)
38	EVA	ss3835887015	Apr 27, 2020 (154)
39	SGDP_PRJ	ss3890051152	Apr 27, 2020 (154)
40	KRGDB	ss3940396419	Apr 27, 2020 (154)
41	KOGIC	ss3983138968	Apr 27, 2020 (154)
42	TOPMED	ss5102396496	Apr 27, 2021 (155)
43	TOMMO_GENOMICS	ss5231633779	Apr 27, 2021 (155)
44	1000G_HIGH_COVERAGE	ss5310298529	Oct 16, 2022 (156)
45	EVA	ss5440034127	Oct 16, 2022 (156)
46	HUGCELL_USP	ss5502339045	Oct 16, 2022 (156)
47	1000G_HIGH_COVERAGE	ss5617478344	Oct 16, 2022 (156)
48	SANFORD_IMAGENETICS	ss5664060883	Oct 16, 2022 (156)
49	TOMMO_GENOMICS	ss5792175047	Oct 16, 2022 (156)
50	YY_MCH	ss5818464586	Oct 16, 2022 (156)
51	EVA	ss5839073020	Oct 16, 2022 (156)
52	EVA	ss5853316085	Oct 16, 2022 (156)
53	EVA	ss5892449446	Oct 16, 2022 (156)
54	EVA	ss5958958504	Oct 16, 2022 (156)
55	1000Genomes	NC_000021.8 - 42081520	Oct 12, 2018 (152)
56	1000Genomes_30x	NC_000021.9 - 40709594	Oct 16, 2022 (156)
57	The Avon Longitudinal Study of Parents and Children Submission ignored due to conflicting rows: Row 44223445 (NC_000021.8:42081519:C:C 2938/3854, NC_000021.8:42081519:C:G 916/3854) Row 44223446 (NC_000021.8:42081519:C:C 3851/3854, NC_000021.8:42081519:C:A 3/3854)	-	Oct 12, 2018 (152)
58	The Avon Longitudinal Study of Parents and Children Submission ignored due to conflicting rows: Row 44223445 (NC_000021.8:42081519:C:C 2938/3854, NC_000021.8:42081519:C:G 916/3854) Row 44223446 (NC_000021.8:42081519:C:C 3851/3854, NC_000021.8:42081519:C:A 3/3854)	-	Oct 12, 2018 (152)
59	Genetic variation in the Estonian population	NC_000021.8 - 42081520	Oct 12, 2018 (152)
60	gnomAD - Genomes Submission ignored due to conflicting rows: Row 563826907 (NC_000021.9:40709593:C:A 51/139958) Row 563826908 (NC_000021.9:40709593:C:G 44150/139888)	-	Apr 27, 2021 (155)
61	gnomAD - Genomes Submission ignored due to conflicting rows: Row 563826907 (NC_000021.9:40709593:C:A 51/139958) Row 563826908 (NC_000021.9:40709593:C:G 44150/139888)	-	Apr 27, 2021 (155)
62	Genome of the Netherlands Release 5	NC_000021.8 - 42081520	Apr 27, 2020 (154)
63	KOREAN population from KRGDB	NC_000021.8 - 42081520	Apr 27, 2020 (154)
64	Korean Genome Project	NC_000021.9 - 40709594	Apr 27, 2020 (154)
65	Northern Sweden Submission ignored due to conflicting rows: Row 17037804 (NC_000021.8:42081519:C:C 477/600, NC_000021.8:42081519:C:G 123/600) Row 17037805 (NC_000021.8:42081519:C:C 597/600, NC_000021.8:42081519:C:A 3/600)	-	Jul 13, 2019 (153)
66	Northern Sweden Submission ignored due to conflicting rows: Row 17037804 (NC_000021.8:42081519:C:C 477/600, NC_000021.8:42081519:C:G 123/600) Row 17037805 (NC_000021.8:42081519:C:C 597/600, NC_000021.8:42081519:C:A 3/600)	-	Jul 13, 2019 (153)
67	Qatari	NC_000021.8 - 42081520	Apr 27, 2020 (154)
68	SGDP_PRJ	NC_000021.8 - 42081520	Apr 27, 2020 (154)
69	Siberian	NC_000021.8 - 42081520	Apr 27, 2020 (154)
70	8.3KJPN	NC_000021.8 - 42081520	Apr 27, 2021 (155)
71	14KJPN	NC_000021.9 - 40709594	Oct 16, 2022 (156)
72	TopMed	NC_000021.9 - 40709594	Apr 27, 2021 (155)
73	UK 10K study - Twins Submission ignored due to conflicting rows: Row 44223445 (NC_000021.8:42081519:C:C 2832/3708, NC_000021.8:42081519:C:G 876/3708) Row 44223446 (NC_000021.8:42081519:C:C 3702/3708, NC_000021.8:42081519:C:A 6/3708)	-	Oct 12, 2018 (152)
74	UK 10K study - Twins Submission ignored due to conflicting rows: Row 44223445 (NC_000021.8:42081519:C:C 2832/3708, NC_000021.8:42081519:C:G 876/3708) Row 44223446 (NC_000021.8:42081519:C:C 3702/3708, NC_000021.8:42081519:C:A 6/3708)	-	Oct 12, 2018 (152)
75	A Vietnamese Genetic Variation Database	NC_000021.8 - 42081520	Jul 13, 2019 (153)
76	ALFA	NC_000021.9 - 40709594	Apr 27, 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)
rs13052038	Sep 24, 2004 (123)
rs111970748	Aug 21, 2014 (142)

Added to this RefSNP Cluster:

Submission IDs	Observation SPDI	Canonical SPDI	Source RSIDs
ss1639610599, ss1682604632, ss2972045776, ss3743752940	NC_000021.8:42081519:C:A	NC_000021.9:40709593:C:A	(self)
13622973288, ss2245959866, ss3707778540	NC_000021.9:40709593:C:A	NC_000021.9:40709593:C:A	(self)
ss78857443, ss91845877, ss204024032, ss283550851, ss292715111	NC_000021.7:41003389:C:G	NC_000021.9:40709593:C:G	(self)
79901517, 31245195, 19699551, 47573813, 20734465, 42068132, 11240858, 89603086, 9758211, ss341032299, ss662421655, ss995142274, ss1082518015, ss1366378022, ss1429191642, ss1639610598, ss1682604631, ss1809698231, ss1938692543, ss2030119534, ss2158724504, ss2629559398, ss2704456147, ss2972045776, ss3018929622, ss3352729906, ss3685506947, ss3743752939, ss3759135981, ss3835887015, ss3890051152, ss3940396419, ss5231633779, ss5440034127, ss5664060883, ss5839073020, ss5958958504	NC_000021.8:42081519:C:G	NC_000021.9:40709593:C:G	(self)
105004279, 39516969, 126012151, 377505442, 13622973288, ss2245959866, ss3651120954, ss3707778541, ss3822303007, ss3983138968, ss5102396496, ss5310298529, ss5502339045, ss5617478344, ss5792175047, ss5818464586, ss5853316085, ss5892449446	NC_000021.9:40709593:C:G	NC_000021.9:40709593:C:G	(self)
ss13569608, ss21832488	NT_011512.9:27741915:C:G	NC_000021.9:40709593:C:G	(self)
ss133097995, ss138320573	NT_011512.11:27743390:C:G	NC_000021.9:40709593:C:G	(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 rs9754270

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

rs9754270