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dbSNP Short Genetic Variations

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.

rs9419461

Current Build 155

Released April 9, 2021

Organism
Homo sapiens
Position
chr10:78827 (GRCh38.p13) 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>T
Variation Type
SNV Single Nucleotide Variation
Frequency
T=0.258767 (35641/137734, GnomAD)
T=0.22866 (5904/25820, ALFA)
T=0.07661 (1284/16760, 8.3KJPN) (+ 9 more)
T=0.2360 (1182/5008, 1000G)
T=0.1124 (329/2928, KOREAN)
T=0.1248 (141/1130, Daghestan)
T=0.186 (186/998, GoNL)
C=0.360 (238/662, HapMap)
T=0.150 (90/600, NorthernSweden)
T=0.218 (47/216, Qatari)
C=0.359 (69/192, SGDP_PRJ)
C=0.42 (5/12, Siberian)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
None
Publications
0 citations
Genomic View
See rs on genome
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.p13 chr 10 NC_000010.11:g.78827C>T
GRCh37.p13 chr 10 NC_000010.10:g.124767C>T
TUBB8 RefSeqGene NG_046777.1:g.2629G>A
GRCh37.p13 chr 10 fix patch HG905_PATCH NW_003571043.1:g.68827C>T
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

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: 20201027095038
Population Group Sample Size Ref Allele Alt Allele
Total Global 25820 C=0.77134 T=0.22866
European Sub 18464 C=0.85187 T=0.14813
African Sub 5578 C=0.4910 T=0.5090
African Others Sub 196 C=0.464 T=0.536
African American Sub 5382 C=0.4920 T=0.5080
Asian Sub 114 C=0.921 T=0.079
East Asian Sub 88 C=0.93 T=0.07
Other Asian Sub 26 C=0.88 T=0.12
Latin American 1 Sub 146 C=0.795 T=0.205
Latin American 2 Sub 610 C=0.848 T=0.152
South Asian Sub 100 C=0.89 T=0.11
Other Sub 808 C=0.769 T=0.231


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
gnomAD - Genomes Global Study-wide 137734 C=0.741233 T=0.258767
gnomAD - Genomes European Sub 74664 C=0.85317 T=0.14683
gnomAD - Genomes African Sub 41274 C=0.49140 T=0.50860
gnomAD - Genomes American Sub 13342 C=0.82289 T=0.17711
gnomAD - Genomes Ashkenazi Jewish Sub 3244 C=0.8699 T=0.1301
gnomAD - Genomes East Asian Sub 3118 C=0.8733 T=0.1267
gnomAD - Genomes Other Sub 2092 C=0.7581 T=0.2419
8.3KJPN JAPANESE Study-wide 16760 C=0.92339 T=0.07661
1000Genomes Global Study-wide 5008 C=0.7640 T=0.2360
1000Genomes African Sub 1322 C=0.4501 T=0.5499
1000Genomes East Asian Sub 1008 C=0.8869 T=0.1131
1000Genomes Europe Sub 1006 C=0.8738 T=0.1262
1000Genomes South Asian Sub 978 C=0.918 T=0.082
1000Genomes American Sub 694 C=0.807 T=0.193
KOREAN population from KRGDB KOREAN Study-wide 2928 C=0.8876 T=0.1124
Genome-wide autozygosity in Daghestan Global Study-wide 1130 C=0.8752 T=0.1248
Genome-wide autozygosity in Daghestan Daghestan Sub 624 C=0.881 T=0.119
Genome-wide autozygosity in Daghestan Near_East Sub 144 C=0.812 T=0.188
Genome-wide autozygosity in Daghestan Central Asia Sub 122 C=0.852 T=0.148
Genome-wide autozygosity in Daghestan Europe Sub 106 C=0.896 T=0.104
Genome-wide autozygosity in Daghestan South Asian Sub 98 C=0.92 T=0.08
Genome-wide autozygosity in Daghestan Caucasus Sub 36 C=0.92 T=0.08
Genome of the Netherlands Release 5 Genome of the Netherlands Study-wide 998 C=0.814 T=0.186
HapMap Global Study-wide 662 C=0.360 T=0.640
HapMap American Sub 292 C=0.360 T=0.640
HapMap Europe Sub 176 C=0.011 T=0.989
HapMap African Sub 110 C=0.455 T=0.545
HapMap Asian Sub 84 C=0.96 T=0.04
Northern Sweden ACPOP Study-wide 600 C=0.850 T=0.150
Qatari Global Study-wide 216 C=0.782 T=0.218
SGDP_PRJ Global Study-wide 192 C=0.359 T=0.641
Siberian Global Study-wide 12 C=0.42 T=0.58
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 C= T
GRCh38.p13 chr 10 NC_000010.11:g.78827= NC_000010.11:g.78827C>T
GRCh37.p13 chr 10 NC_000010.10:g.124767= NC_000010.10:g.124767C>T
TUBB8 RefSeqGene NG_046777.1:g.2629= NG_046777.1:g.2629G>A
GRCh37.p13 chr 10 fix patch HG905_PATCH NW_003571043.1:g.68827= NW_003571043.1:g.68827C>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#.

51 SubSNP, 12 Frequency submissions
No Submitter Submission ID Date (Build)
1 SC_SNP ss12973096 Dec 05, 2003 (119)
2 SSAHASNP ss20720188 Apr 05, 2004 (121)
3 ABI ss39729894 Mar 15, 2006 (126)
4 ILLUMINA ss75297982 Dec 07, 2007 (129)
5 HUMANGENOME_JCVI ss97613045 Feb 06, 2009 (130)
6 1000GENOMES ss109145707 Jan 23, 2009 (130)
7 ILLUMINA-UK ss118963200 Feb 15, 2009 (130)
8 ILLUMINA ss123373652 Dec 01, 2009 (131)
9 ENSEMBL ss131842101 Dec 01, 2009 (131)
10 ILLUMINA ss154493330 Dec 01, 2009 (131)
11 GMI ss158077292 Dec 01, 2009 (131)
12 ILLUMINA ss160986239 Dec 01, 2009 (131)
13 ILLUMINA ss172463153 Jul 04, 2010 (132)
14 ILLUMINA ss174840042 Jul 04, 2010 (132)
15 BUSHMAN ss201023248 Jul 04, 2010 (132)
16 BCM-HGSC-SUB ss207296758 Jul 04, 2010 (132)
17 1000GENOMES ss224512314 Jul 14, 2010 (132)
18 1000GENOMES ss235012219 Jul 15, 2010 (132)
19 1000GENOMES ss241753199 Jul 15, 2010 (132)
20 GMI ss280440361 May 04, 2012 (137)
21 PJP ss290815777 May 09, 2011 (134)
22 ILLUMINA ss482887221 Sep 11, 2015 (146)
23 TISHKOFF ss561707903 Apr 25, 2013 (138)
24 SSMP ss656208227 Apr 25, 2013 (138)
25 ILLUMINA ss825669004 Apr 01, 2015 (144)
26 EVA-GONL ss987096706 Aug 21, 2014 (142)
27 JMKIDD_LAB ss1076687371 Aug 21, 2014 (142)
28 1000GENOMES ss1335912617 Aug 21, 2014 (142)
29 HAMMER_LAB ss1397569555 Sep 08, 2015 (146)
30 HAMMER_LAB ss1806212530 Sep 11, 2015 (146)
31 WEILL_CORNELL_DGM ss1930414686 Feb 17, 2016 (147)
32 JJLAB ss2025929533 Sep 28, 2016 (149)
33 USC_VALOUEV ss2154169582 Oct 12, 2018 (152)
34 TOPMED ss2334634756 Oct 12, 2018 (152)
35 SYSTEMSBIOZJU ss2627432608 Oct 12, 2018 (152)
36 GRF ss2698388980 Oct 12, 2018 (152)
37 GNOMAD ss2884518245 Oct 12, 2018 (152)
38 SWEGEN ss3005784241 Oct 12, 2018 (152)
39 TOPMED ss3109330500 Nov 08, 2017 (151)
40 ILLUMINA ss3636064872 Oct 12, 2018 (152)
41 ILLUMINA ss3642833506 Oct 12, 2018 (152)
42 URBANLAB ss3649265480 Oct 12, 2018 (152)
43 EVA_DECODE ss3689095221 Jul 13, 2019 (153)
44 ACPOP ss3736974254 Jul 13, 2019 (153)
45 EVA ss3747627259 Jul 13, 2019 (153)
46 KHV_HUMAN_GENOMES ss3812993247 Jul 13, 2019 (153)
47 EVA ss3831916708 Apr 26, 2020 (154)
48 SGDP_PRJ ss3873326300 Apr 26, 2020 (154)
49 KRGDB ss3921253270 Apr 26, 2020 (154)
50 GNOMAD ss4211408731 Apr 26, 2021 (155)
51 TOMMO_GENOMICS ss5195847774 Apr 26, 2021 (155)
52 1000Genomes NC_000010.10 - 124767 Oct 12, 2018 (152)
53 Genome-wide autozygosity in Daghestan NC_000010.9 - 114767 Apr 26, 2020 (154)
54 gnomAD - Genomes NC_000010.11 - 78827 Apr 26, 2021 (155)
55 Genome of the Netherlands Release 5 NC_000010.10 - 124767 Apr 26, 2020 (154)
56 HapMap NC_000010.11 - 78827 Apr 26, 2020 (154)
57 KOREAN population from KRGDB NC_000010.10 - 124767 Apr 26, 2020 (154)
58 Northern Sweden NC_000010.10 - 124767 Jul 13, 2019 (153)
59 Qatari NC_000010.10 - 124767 Apr 26, 2020 (154)
60 SGDP_PRJ NC_000010.10 - 124767 Apr 26, 2020 (154)
61 Siberian NC_000010.10 - 124767 Apr 26, 2020 (154)
62 8.3KJPN NC_000010.10 - 124767 Apr 26, 2021 (155)
63 ALFA NC_000010.11 - 78827 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
41179, ss109145707, ss118963200, ss201023248, ss207296758, ss280440361, ss290815777, ss825669004, ss1397569555, ss3642833506 NC_000010.9:114766:C:T NC_000010.11:78826:C:T (self)
48246312, 11953833, 28430664, 10259119, 12456616, 25343280, 6685936, 53817081, ss224512314, ss235012219, ss241753199, ss482887221, ss561707903, ss656208227, ss987096706, ss1076687371, ss1335912617, ss1806212530, ss1930414686, ss2025929533, ss2154169582, ss2334634756, ss2627432608, ss2698388980, ss2884518245, ss3005784241, ss3636064872, ss3736974254, ss3747627259, ss3831916708, ss3873326300, ss3921253270, ss5195847774 NC_000010.10:124766:C:T NC_000010.11:78826:C:T (self)
340931906, 317095, 34601135, 9966281744, ss3109330500, ss3649265480, ss3689095221, ss3812993247, ss4211408731 NC_000010.11:78826:C:T NC_000010.11:78826:C:T (self)
ss39729894, ss75297982, ss97613045, ss123373652, ss131842101, ss154493330, ss158077292, ss160986239, ss172463153, ss174840042 NT_008705.16:64766:C:T NC_000010.11:78826:C:T (self)
ss12973096 NT_024115.14:64766:C:T NC_000010.11:78826:C:T (self)
ss20720188 NT_077567.3:64766:C:T NC_000010.11:78826:C:T (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 rs9419461

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.post596+ae089ad