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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.

rs17101444

Current Build 155

Released April 9, 2021

Organism
Homo sapiens
Position
chr1:83189694 (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
G>A
Variation Type
SNV Single Nucleotide Variation
Frequency
A=0.002063 (277/134272, GnomAD)
A=0.04755 (1231/25888, ALFA)
A=0.00072 (12/16760, 8.3KJPN) (+ 7 more)
A=0.0014 (4/2922, KOREAN)
A=0.080 (80/998, GoNL)
A=0.015 (9/600, NorthernSweden)
A=0.118 (37/314, HapMap)
A=0.093 (20/216, Qatari)
G=0.50 (19/38, SGDP_PRJ)
A=0.50 (19/38, SGDP_PRJ)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
LOC107985037 : Intron Variant
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 1 NC_000001.11:g.83189694G>A
GRCh37.p13 chr 1 NC_000001.10:g.83655377G>A
Gene: LOC107985037, uncharacterized LOC107985037 (minus strand)
Molecule type Change Amino acid[Codon] SO Term
LOC107985037 transcript XR_001738121.1: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

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 25888 G=0.95245 A=0.04755
European Sub 16808 G=0.96490 A=0.03510
African Sub 4502 G=0.9340 A=0.0660
African Others Sub 166 G=0.958 A=0.042
African American Sub 4336 G=0.9331 A=0.0669
Asian Sub 146 G=0.993 A=0.007
East Asian Sub 114 G=0.991 A=0.009
Other Asian Sub 32 G=1.00 A=0.00
Latin American 1 Sub 482 G=0.873 A=0.127
Latin American 2 Sub 666 G=0.974 A=0.026
South Asian Sub 140 G=0.950 A=0.050
Other Sub 3144 G=0.9179 A=0.0821


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").

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Study Population Group Sample Size Ref Allele Alt Allele
gnomAD - Genomes Global Study-wide 134272 G=0.997937 A=0.002063
gnomAD - Genomes European Sub 73534 G=0.99879 A=0.00121
gnomAD - Genomes African Sub 39312 G=0.99664 A=0.00336
gnomAD - Genomes American Sub 13010 G=0.99700 A=0.00300
gnomAD - Genomes Ashkenazi Jewish Sub 3250 G=0.9969 A=0.0031
gnomAD - Genomes East Asian Sub 3116 G=1.0000 A=0.0000
gnomAD - Genomes Other Sub 2050 G=0.9966 A=0.0034
Allele Frequency Aggregator Total Global 25888 G=0.95245 A=0.04755
Allele Frequency Aggregator European Sub 16808 G=0.96490 A=0.03510
Allele Frequency Aggregator African Sub 4502 G=0.9340 A=0.0660
Allele Frequency Aggregator Other Sub 3144 G=0.9179 A=0.0821
Allele Frequency Aggregator Latin American 2 Sub 666 G=0.974 A=0.026
Allele Frequency Aggregator Latin American 1 Sub 482 G=0.873 A=0.127
Allele Frequency Aggregator Asian Sub 146 G=0.993 A=0.007
Allele Frequency Aggregator South Asian Sub 140 G=0.950 A=0.050
8.3KJPN JAPANESE Study-wide 16760 G=0.99928 A=0.00072
KOREAN population from KRGDB KOREAN Study-wide 2922 G=0.9986 A=0.0014
Genome of the Netherlands Release 5 Genome of the Netherlands Study-wide 998 G=0.920 A=0.080
Northern Sweden ACPOP Study-wide 600 G=0.985 A=0.015
HapMap Global Study-wide 314 G=0.882 A=0.118
HapMap American Sub 116 G=0.922 A=0.078
HapMap African Sub 114 G=0.798 A=0.202
HapMap Asian Sub 84 G=0.94 A=0.06
Qatari Global Study-wide 216 G=0.907 A=0.093
SGDP_PRJ Global Study-wide 38 G=0.50 A=0.50
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.p13 chr 1 NC_000001.11:g.83189694= NC_000001.11:g.83189694G>A
GRCh37.p13 chr 1 NC_000001.10:g.83655377= NC_000001.10:g.83655377G>A
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#.

24 SubSNP, 9 Frequency submissions
No Submitter Submission ID Date (Build)
1 PERLEGEN ss23145058 Sep 20, 2004 (123)
2 ILLUMINA-UK ss118850896 Feb 14, 2009 (142)
3 ENSEMBL ss143082980 Dec 01, 2009 (142)
4 ILLUMINA ss160423584 Dec 01, 2009 (131)
5 1000GENOMES ss218492134 Jul 14, 2010 (132)
6 1000GENOMES ss230613044 Jul 14, 2010 (132)
7 1000GENOMES ss238291087 Jul 15, 2010 (132)
8 ILLUMINA ss480910680 Sep 08, 2015 (146)
9 SSMP ss648176841 Apr 25, 2013 (138)
10 EVA-GONL ss975366435 Aug 21, 2014 (142)
11 DDI ss1425876509 Apr 01, 2015 (144)
12 WEILL_CORNELL_DGM ss1918569496 Feb 12, 2016 (147)
13 ILLUMINA ss1958288245 Feb 12, 2016 (147)
14 GNOMAD ss2757371962 Nov 08, 2017 (151)
15 ILLUMINA ss3021104408 Nov 08, 2017 (151)
16 TOPMED ss3081753910 Nov 08, 2017 (151)
17 CSHL ss3343544226 Nov 08, 2017 (151)
18 ILLUMINA ss3636010697 Oct 11, 2018 (152)
19 ILLUMINA ss3651432844 Oct 11, 2018 (152)
20 ACPOP ss3727217855 Jul 12, 2019 (153)
21 EVA ss3746441338 Jul 12, 2019 (153)
22 SGDP_PRJ ss3849252280 Apr 25, 2020 (154)
23 KRGDB ss3894303771 Apr 25, 2020 (154)
24 TOMMO_GENOMICS ss5144815644 Apr 25, 2021 (155)
25 gnomAD - Genomes NC_000001.11 - 83189694 Apr 25, 2021 (155)
26 Genome of the Netherlands Release 5 NC_000001.10 - 83655377 Apr 25, 2020 (154)
27 HapMap NC_000001.11 - 83189694 Apr 25, 2020 (154)
28 KOREAN population from KRGDB NC_000001.10 - 83655377 Apr 25, 2020 (154)
29 Northern Sweden NC_000001.10 - 83655377 Jul 12, 2019 (153)
30 Qatari NC_000001.10 - 83655377 Apr 25, 2020 (154)
31 SGDP_PRJ NC_000001.10 - 83655377 Apr 25, 2020 (154)
32 8.3KJPN NC_000001.10 - 83655377 Apr 25, 2021 (155)
33 ALFA NC_000001.11 - 83189694 Apr 25, 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).

Associated ID History Updated (Build)
rs74096273 Aug 21, 2014 (142)
Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
ss118850896 NC_000001.9:83427964:G:A NC_000001.11:83189693:G:A (self)
573376, 1481165, 502720, 611426, 1269260, 2784951, ss218492134, ss230613044, ss238291087, ss480910680, ss648176841, ss975366435, ss1425876509, ss1918569496, ss1958288245, ss2757371962, ss3021104408, ss3343544226, ss3636010697, ss3651432844, ss3727217855, ss3746441338, ss3849252280, ss3894303771, ss5144815644 NC_000001.10:83655376:G:A NC_000001.11:83189693:G:A (self)
17076612, 113098, 1107023234, ss3081753910 NC_000001.11:83189693:G:A NC_000001.11:83189693:G:A (self)
ss23145058, ss143082980, ss160423584 NT_032977.9:53627294:G:A NC_000001.11:83189693: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 rs17101444

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