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dbSNP Short Genetic Variations

Examples: rs268, BRCA1 and more Advanced search

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.

rs62223481

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr21:38100488 (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
G>A
Variation Type
SNV Single Nucleotide Variation
Frequency
A=0.020050 (5307/264690, TOPMED)
A=0.019220 (2695/140216, GnomAD)
A=0.02414 (456/18890, ALFA) (+ 12 more)
A=0.0105 (67/6404, 1000G_30x)
A=0.0100 (50/5008, 1000G)
A=0.0243 (109/4480, Estonian)
A=0.0317 (122/3854, ALSPAC)
A=0.0262 (97/3708, TWINSUK)
A=0.024 (24/998, GoNL)
A=0.007 (4/600, NorthernSweden)
A=0.042 (9/216, Qatari)
G=0.50 (10/20, SGDP_PRJ)
A=0.50 (10/20, SGDP_PRJ)
G=0.5 (1/2, Siberian)
A=0.5 (1/2, Siberian)
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 G=0.97586 A=0.02414
European Sub 14286 G=0.97123 A=0.02877
African Sub 2946 G=0.9936 A=0.0064
African Others Sub 114 G=1.000 A=0.000
African American Sub 2832 G=0.9933 A=0.0067
Asian Sub 112 G=1.000 A=0.000
East Asian Sub 86 G=1.00 A=0.00
Other Asian Sub 26 G=1.00 A=0.00
Latin American 1 Sub 146 G=0.966 A=0.034
Latin American 2 Sub 610 G=0.990 A=0.010
South Asian Sub 98 G=0.99 A=0.01
Other Sub 692 G=0.980 A=0.020


Help

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").

Download
Study Population Group Sample Size Ref Allele Alt Allele
TopMed Global Study-wide 264690 G=0.979950 A=0.020050
gnomAD - Genomes Global Study-wide 140216 G=0.980780 A=0.019220
gnomAD - Genomes European Sub 75932 G=0.97494 A=0.02506
gnomAD - Genomes African Sub 42028 G=0.99339 A=0.00661
gnomAD - Genomes American Sub 13650 G=0.97399 A=0.02601
gnomAD - Genomes Ashkenazi Jewish Sub 3320 G=0.9639 A=0.0361
gnomAD - Genomes East Asian Sub 3132 G=1.0000 A=0.0000
gnomAD - Genomes Other Sub 2154 G=0.9819 A=0.0181
Allele Frequency Aggregator Total Global 18890 G=0.97586 A=0.02414
Allele Frequency Aggregator European Sub 14286 G=0.97123 A=0.02877
Allele Frequency Aggregator African Sub 2946 G=0.9936 A=0.0064
Allele Frequency Aggregator Other Sub 692 G=0.980 A=0.020
Allele Frequency Aggregator Latin American 2 Sub 610 G=0.990 A=0.010
Allele Frequency Aggregator Latin American 1 Sub 146 G=0.966 A=0.034
Allele Frequency Aggregator Asian Sub 112 G=1.000 A=0.000
Allele Frequency Aggregator South Asian Sub 98 G=0.99 A=0.01
1000Genomes_30x Global Study-wide 6404 G=0.9895 A=0.0105
1000Genomes_30x African Sub 1786 G=1.0000 A=0.0000
1000Genomes_30x Europe Sub 1266 G=0.9739 A=0.0261
1000Genomes_30x South Asian Sub 1202 G=0.9942 A=0.0058
1000Genomes_30x East Asian Sub 1170 G=0.9983 A=0.0017
1000Genomes_30x American Sub 980 G=0.974 A=0.026
1000Genomes Global Study-wide 5008 G=0.9900 A=0.0100
1000Genomes African Sub 1322 G=1.0000 A=0.0000
1000Genomes East Asian Sub 1008 G=0.9980 A=0.0020
1000Genomes Europe Sub 1006 G=0.9732 A=0.0268
1000Genomes South Asian Sub 978 G=0.996 A=0.004
1000Genomes American Sub 694 G=0.976 A=0.024
Genetic variation in the Estonian population Estonian Study-wide 4480 G=0.9757 A=0.0243
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 G=0.9683 A=0.0317
UK 10K study - Twins TWIN COHORT Study-wide 3708 G=0.9738 A=0.0262
Genome of the Netherlands Release 5 Genome of the Netherlands Study-wide 998 G=0.976 A=0.024
Northern Sweden ACPOP Study-wide 600 G=0.993 A=0.007
Qatari Global Study-wide 216 G=0.958 A=0.042
SGDP_PRJ Global Study-wide 20 G=0.50 A=0.50
Siberian Global Study-wide 2 G=0.5 A=0.5
Help

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.38100488G>A
GRCh37.p13 chr 21 NC_000021.8:g.39472582G>A
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
Help

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
Help

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 G= A
GRCh38.p14 chr 21 NC_000021.9:g.38100488= NC_000021.9:g.38100488G>A
GRCh37.p13 chr 21 NC_000021.8:g.39472582= NC_000021.8:g.39472582G>A
DSCR4 transcript NM_005867.2:c.230+19819= NM_005867.2:c.230+19819C>T
Help

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#.

33 SubSNP, 13 Frequency submissions
No Submitter Submission ID Date (Build)
1 BCMHGSC_JDW ss91837904 Mar 24, 2008 (129)
2 ENSEMBL ss138316607 Dec 01, 2009 (131)
3 1000GENOMES ss237982164 Jul 15, 2010 (132)
4 TISHKOFF ss566495978 Apr 25, 2013 (138)
5 SSMP ss662406420 Apr 25, 2013 (138)
6 EVA-GONL ss995120406 Aug 21, 2014 (142)
7 JMKIDD_LAB ss1082500669 Aug 21, 2014 (142)
8 1000GENOMES ss1366298620 Aug 21, 2014 (142)
9 EVA_UK10K_ALSPAC ss1639566583 Apr 01, 2015 (144)
10 EVA_UK10K_TWINSUK ss1682560616 Apr 01, 2015 (144)
11 EVA_DECODE ss1699190812 Apr 01, 2015 (144)
12 WEILL_CORNELL_DGM ss1938670452 Feb 12, 2016 (147)
13 JJLAB ss2030107221 Sep 14, 2016 (149)
14 USC_VALOUEV ss2158712125 Dec 20, 2016 (150)
15 HUMAN_LONGEVITY ss2245796954 Dec 20, 2016 (150)
16 GNOMAD ss2971829635 Nov 08, 2017 (151)
17 SWEGEN ss3018896240 Nov 08, 2017 (151)
18 CSHL ss3352719521 Nov 08, 2017 (151)
19 EGCUT_WGS ss3685473218 Jul 13, 2019 (153)
20 EVA_DECODE ss3707736451 Jul 13, 2019 (153)
21 ACPOP ss3743734081 Jul 13, 2019 (153)
22 EVA ss3759110333 Jul 13, 2019 (153)
23 SGDP_PRJ ss3890007035 Apr 27, 2020 (154)
24 TOPMED ss5101727832 Apr 26, 2021 (155)
25 1000G_HIGH_COVERAGE ss5310228188 Oct 13, 2022 (156)
26 EVA ss5439907077 Oct 13, 2022 (156)
27 HUGCELL_USP ss5502274698 Oct 13, 2022 (156)
28 1000G_HIGH_COVERAGE ss5617376065 Oct 13, 2022 (156)
29 SANFORD_IMAGENETICS ss5664019551 Oct 13, 2022 (156)
30 YY_MCH ss5818446160 Oct 13, 2022 (156)
31 EVA ss5839044601 Oct 13, 2022 (156)
32 EVA ss5892367866 Oct 13, 2022 (156)
33 EVA ss5958915355 Oct 13, 2022 (156)
34 1000Genomes NC_000021.8 - 39472582 Oct 12, 2018 (152)
35 1000Genomes_30x NC_000021.9 - 38100488 Oct 13, 2022 (156)
36 The Avon Longitudinal Study of Parents and Children NC_000021.8 - 39472582 Oct 12, 2018 (152)
37 Genetic variation in the Estonian population NC_000021.8 - 39472582 Oct 12, 2018 (152)
38 gnomAD - Genomes NC_000021.9 - 38100488 Apr 26, 2021 (155)
39 Genome of the Netherlands Release 5 NC_000021.8 - 39472582 Apr 27, 2020 (154)
40 Northern Sweden NC_000021.8 - 39472582 Jul 13, 2019 (153)
41 Qatari NC_000021.8 - 39472582 Apr 27, 2020 (154)
42 SGDP_PRJ NC_000021.8 - 39472582 Apr 27, 2020 (154)
43 Siberian NC_000021.8 - 39472582 Apr 27, 2020 (154)
44 TopMed NC_000021.9 - 38100488 Apr 26, 2021 (155)
45 UK 10K study - Twins NC_000021.8 - 39472582 Oct 12, 2018 (152)
46 ALFA NC_000021.9 - 38100488 Apr 26, 2021 (155)
Help

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
ss91837904, ss1699190812 NC_000021.7:38394451:G:A NC_000021.9:38100487:G:A (self)
79818919, 44174784, 31211466, 19678174, 17018946, 20712374, 42024015, 11228479, 44174784, ss237982164, ss566495978, ss662406420, ss995120406, ss1082500669, ss1366298620, ss1639566583, ss1682560616, ss1938670452, ss2030107221, ss2158712125, ss2971829635, ss3018896240, ss3352719521, ss3685473218, ss3743734081, ss3759110333, ss3890007035, ss5439907077, ss5664019551, ss5839044601, ss5958915355 NC_000021.8:39472581:G:A NC_000021.9:38100487:G:A (self)
104902000, 563281421, 376836778, 9023220698, ss2245796954, ss3707736451, ss5101727832, ss5310228188, ss5502274698, ss5617376065, ss5818446160, ss5892367866 NC_000021.9:38100487:G:A NC_000021.9:38100487:G:A (self)
ss138316607 NT_011512.11:25134452:G:A NC_000021.9:38100487:G:A (self)
Help

Publications tab displays PubMed articles citing the variation as a listing of PMID, Title, Author, Year, Journal, ordered by Year, descending.

No publications for rs62223481

Help

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.

Software version is: 2.0.1.post761+d5e8e07