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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.

rs9578851

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr13:25372569 (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>C
Variation Type
SNV Single Nucleotide Variation
Frequency
C=0.109252 (28918/264690, TOPMED)
C=0.097996 (13733/140138, GnomAD)
C=0.06416 (1813/28256, 14KJPN) (+ 10 more)
C=0.06274 (1162/18520, ALFA)
C=0.06422 (1076/16756, 8.3KJPN)
C=0.1335 (855/6404, 1000G_30x)
C=0.1278 (640/5008, 1000G)
C=0.0174 (78/4480, Estonian)
C=0.0786 (229/2914, KOREAN)
C=0.0860 (154/1790, Korea1K)
C=0.003 (2/600, NorthernSweden)
C=0.074 (16/216, Qatari)
G=0.45 (37/82, SGDP_PRJ)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
ATP8A2 : 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 18520 G=0.93726 C=0.06274
European Sub 14152 G=0.97852 C=0.02148
African Sub 2898 G=0.7602 C=0.2398
African Others Sub 114 G=0.675 C=0.325
African American Sub 2784 G=0.7636 C=0.2364
Asian Sub 112 G=0.946 C=0.054
East Asian Sub 86 G=0.97 C=0.03
Other Asian Sub 26 G=0.88 C=0.12
Latin American 1 Sub 146 G=0.870 C=0.130
Latin American 2 Sub 610 G=0.879 C=0.121
South Asian Sub 98 G=0.92 C=0.08
Other Sub 504 G=0.889 C=0.111


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=0.890748 C=0.109252
gnomAD - Genomes Global Study-wide 140138 G=0.902004 C=0.097996
gnomAD - Genomes European Sub 75924 G=0.97750 C=0.02250
gnomAD - Genomes African Sub 41946 G=0.75828 C=0.24172
gnomAD - Genomes American Sub 13660 G=0.90286 C=0.09714
gnomAD - Genomes Ashkenazi Jewish Sub 3324 G=0.9654 C=0.0346
gnomAD - Genomes East Asian Sub 3132 G=0.9199 C=0.0801
gnomAD - Genomes Other Sub 2152 G=0.9103 C=0.0897
14KJPN JAPANESE Study-wide 28256 G=0.93584 C=0.06416
Allele Frequency Aggregator Total Global 18520 G=0.93726 C=0.06274
Allele Frequency Aggregator European Sub 14152 G=0.97852 C=0.02148
Allele Frequency Aggregator African Sub 2898 G=0.7602 C=0.2398
Allele Frequency Aggregator Latin American 2 Sub 610 G=0.879 C=0.121
Allele Frequency Aggregator Other Sub 504 G=0.889 C=0.111
Allele Frequency Aggregator Latin American 1 Sub 146 G=0.870 C=0.130
Allele Frequency Aggregator Asian Sub 112 G=0.946 C=0.054
Allele Frequency Aggregator South Asian Sub 98 G=0.92 C=0.08
8.3KJPN JAPANESE Study-wide 16756 G=0.93578 C=0.06422
1000Genomes_30x Global Study-wide 6404 G=0.8665 C=0.1335
1000Genomes_30x African Sub 1786 G=0.7111 C=0.2889
1000Genomes_30x Europe Sub 1266 G=0.9795 C=0.0205
1000Genomes_30x South Asian Sub 1202 G=0.9135 C=0.0865
1000Genomes_30x East Asian Sub 1170 G=0.9188 C=0.0812
1000Genomes_30x American Sub 980 G=0.884 C=0.116
1000Genomes Global Study-wide 5008 G=0.8722 C=0.1278
1000Genomes African Sub 1322 G=0.7209 C=0.2791
1000Genomes East Asian Sub 1008 G=0.9157 C=0.0843
1000Genomes Europe Sub 1006 G=0.9791 C=0.0209
1000Genomes South Asian Sub 978 G=0.914 C=0.086
1000Genomes American Sub 694 G=0.883 C=0.117
Genetic variation in the Estonian population Estonian Study-wide 4480 G=0.9826 C=0.0174
KOREAN population from KRGDB KOREAN Study-wide 2914 G=0.9214 C=0.0786
Korean Genome Project KOREAN Study-wide 1790 G=0.9140 C=0.0860
Northern Sweden ACPOP Study-wide 600 G=0.997 C=0.003
Qatari Global Study-wide 216 G=0.926 C=0.074
SGDP_PRJ Global Study-wide 82 G=0.45 C=0.55
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 13 NC_000013.11:g.25372569G>C
GRCh37.p13 chr 13 NC_000013.10:g.25946707G>C
ATP8A2 RefSeqGene NG_042855.1:g.5559G>C
Gene: ATP8A2, ATPase phospholipid transporting 8A2 (plus strand)
Molecule type Change Amino acid[Codon] SO Term
ATP8A2 transcript variant 1 NM_016529.6:c.76+281G>C N/A Intron Variant
ATP8A2 transcript variant 2 NM_001313741.1:c. N/A Genic Upstream Transcript Variant
ATP8A2 transcript variant X1 XM_011535103.2:c.76+281G>C N/A Intron Variant
ATP8A2 transcript variant X5 XM_011535106.2:c.76+281G>C N/A Intron Variant
ATP8A2 transcript variant X4 XM_011535107.4:c.76+281G>C N/A Intron Variant
ATP8A2 transcript variant X7 XM_011535113.3:c.76+281G>C N/A Intron Variant
ATP8A2 transcript variant X8 XM_017020625.3:c.76+281G>C N/A Intron Variant
ATP8A2 transcript variant X9 XM_017020626.2:c.76+281G>C N/A Intron Variant
ATP8A2 transcript variant X1 XM_005266419.2:c. N/A Genic Upstream Transcript Variant
ATP8A2 transcript variant X2 XM_011535104.3:c. N/A Genic Upstream Transcript Variant
ATP8A2 transcript variant X5 XM_011535109.4:c. N/A Genic Upstream Transcript Variant
ATP8A2 transcript variant X6 XM_024449369.1:c. N/A Genic Upstream Transcript Variant
ATP8A2 transcript variant X3 XM_047430383.1:c. N/A Genic Upstream Transcript 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= C
GRCh38.p14 chr 13 NC_000013.11:g.25372569= NC_000013.11:g.25372569G>C
GRCh37.p13 chr 13 NC_000013.10:g.25946707= NC_000013.10:g.25946707G>C
ATP8A2 RefSeqGene NG_042855.1:g.5559= NG_042855.1:g.5559G>C
ATP8A2 transcript NM_016529.4:c.76+281= NM_016529.4:c.76+281G>C
ATP8A2 transcript variant 1 NM_016529.6:c.76+281= NM_016529.6:c.76+281G>C
ATP8A2 transcript variant X1 XM_011535103.2:c.76+281= XM_011535103.2:c.76+281G>C
ATP8A2 transcript variant X5 XM_011535106.2:c.76+281= XM_011535106.2:c.76+281G>C
ATP8A2 transcript variant X4 XM_011535107.4:c.76+281= XM_011535107.4:c.76+281G>C
ATP8A2 transcript variant X7 XM_011535113.3:c.76+281= XM_011535113.3:c.76+281G>C
ATP8A2 transcript variant X8 XM_017020625.3:c.76+281= XM_017020625.3:c.76+281G>C
ATP8A2 transcript variant X9 XM_017020626.2:c.76+281= XM_017020626.2:c.76+281G>C
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#.

32 SubSNP, 13 Frequency submissions
No Submitter Submission ID Date (Build)
1 SC_SNP ss13303934 Dec 05, 2003 (119)
2 1000GENOMES ss211375557 Jul 14, 2010 (132)
3 1000GENOMES ss463252185 Sep 17, 2011 (135)
4 1000GENOMES ss1347522895 Aug 21, 2014 (142)
5 EVA_DECODE ss1642306161 Apr 01, 2015 (144)
6 WEILL_CORNELL_DGM ss1933569574 Feb 12, 2016 (147)
7 JJLAB ss2027539405 Sep 14, 2016 (149)
8 HUMAN_LONGEVITY ss2194905605 Dec 20, 2016 (150)
9 GRF ss2700276027 Nov 08, 2017 (151)
10 GNOMAD ss2917678670 Nov 08, 2017 (151)
11 SWEGEN ss3010733943 Nov 08, 2017 (151)
12 EGCUT_WGS ss3677994917 Jul 13, 2019 (153)
13 EVA_DECODE ss3694941159 Jul 13, 2019 (153)
14 ACPOP ss3739589475 Jul 13, 2019 (153)
15 EVA ss3751245009 Jul 13, 2019 (153)
16 KHV_HUMAN_GENOMES ss3816576145 Jul 13, 2019 (153)
17 SGDP_PRJ ss3879609329 Apr 27, 2020 (154)
18 KRGDB ss3928427922 Apr 27, 2020 (154)
19 KOGIC ss3973223147 Apr 27, 2020 (154)
20 TOPMED ss4940185139 Apr 26, 2021 (155)
21 TOMMO_GENOMICS ss5209211282 Apr 26, 2021 (155)
22 1000G_HIGH_COVERAGE ss5293122433 Oct 16, 2022 (156)
23 EVA ss5409651933 Oct 16, 2022 (156)
24 HUGCELL_USP ss5487545928 Oct 16, 2022 (156)
25 1000G_HIGH_COVERAGE ss5591768282 Oct 16, 2022 (156)
26 SANFORD_IMAGENETICS ss5654416650 Oct 16, 2022 (156)
27 TOMMO_GENOMICS ss5760862038 Oct 16, 2022 (156)
28 YY_MCH ss5813957686 Oct 16, 2022 (156)
29 EVA ss5839232131 Oct 16, 2022 (156)
30 EVA ss5850651036 Oct 16, 2022 (156)
31 EVA ss5924398327 Oct 16, 2022 (156)
32 EVA ss5945821040 Oct 16, 2022 (156)
33 1000Genomes NC_000013.10 - 25946707 Oct 12, 2018 (152)
34 1000Genomes_30x NC_000013.11 - 25372569 Oct 16, 2022 (156)
35 Genetic variation in the Estonian population NC_000013.10 - 25946707 Oct 12, 2018 (152)
36 gnomAD - Genomes NC_000013.11 - 25372569 Apr 26, 2021 (155)
37 KOREAN population from KRGDB NC_000013.10 - 25946707 Apr 27, 2020 (154)
38 Korean Genome Project NC_000013.11 - 25372569 Apr 27, 2020 (154)
39 Northern Sweden NC_000013.10 - 25946707 Jul 13, 2019 (153)
40 Qatari NC_000013.10 - 25946707 Apr 27, 2020 (154)
41 SGDP_PRJ NC_000013.10 - 25946707 Apr 27, 2020 (154)
42 8.3KJPN NC_000013.10 - 25946707 Apr 26, 2021 (155)
43 14KJPN NC_000013.11 - 25372569 Oct 16, 2022 (156)
44 TopMed NC_000013.11 - 25372569 Apr 26, 2021 (155)
45 ALFA NC_000013.11 - 25372569 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
ss211375557, ss1642306161 NC_000013.9:24844706:G:C NC_000013.11:25372568:G:C (self)
60367497, 23733165, 35605316, 12874340, 15611504, 31626309, 67180589, ss463252185, ss1347522895, ss1933569574, ss2027539405, ss2700276027, ss2917678670, ss3010733943, ss3677994917, ss3739589475, ss3751245009, ss3879609329, ss3928427922, ss5209211282, ss5409651933, ss5654416650, ss5839232131, ss5945821040 NC_000013.10:25946706:G:C NC_000013.11:25372568:G:C (self)
79294217, 425709460, 29601148, 94699142, 155730797, 9892430477, ss2194905605, ss3694941159, ss3816576145, ss3973223147, ss4940185139, ss5293122433, ss5487545928, ss5591768282, ss5760862038, ss5813957686, ss5850651036, ss5924398327 NC_000013.11:25372568:G:C NC_000013.11:25372568:G:C (self)
ss13303934 NT_009799.12:6926706:G:C NC_000013.11:25372568:G:C (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 rs9578851

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