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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.

rs17109619

Current Build 155

Released April 9, 2021

Organism
Homo sapiens
Position
chr1:83044105 (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
A>C
Variation Type
SNV Single Nucleotide Variation
Frequency
C=0.015981 (4230/264690, TOPMED)
C=0.015200 (2131/140194, GnomAD)
C=0.01089 (157/14420, ALFA) (+ 5 more)
C=0.0178 (89/5008, 1000G)
C=0.009 (2/216, Qatari)
C=0.00 (0/72, Ancient Sardinia)
A=0.5 (1/2, SGDP_PRJ)
C=0.5 (1/2, SGDP_PRJ)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
LINC01362 : Intron Variant
LOC107985037 : 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: 20201027095038
Population Group Sample Size Ref Allele Alt Allele
Total Global 14420 A=0.98911 C=0.01089
European Sub 9824 A=0.9998 C=0.0002
African Sub 2946 A=0.9518 C=0.0482
African Others Sub 114 A=0.939 C=0.061
African American Sub 2832 A=0.9523 C=0.0477
Asian Sub 112 A=1.000 C=0.000
East Asian Sub 86 A=1.00 C=0.00
Other Asian Sub 26 A=1.00 C=0.00
Latin American 1 Sub 146 A=0.973 C=0.027
Latin American 2 Sub 610 A=0.998 C=0.002
South Asian Sub 98 A=1.00 C=0.00
Other Sub 684 A=0.988 C=0.012


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 A=0.984019 C=0.015981
gnomAD - Genomes Global Study-wide 140194 A=0.984800 C=0.015200
gnomAD - Genomes European Sub 75934 A=0.99983 C=0.00017
gnomAD - Genomes African Sub 42014 A=0.95109 C=0.04891
gnomAD - Genomes American Sub 13644 A=0.99729 C=0.00271
gnomAD - Genomes Ashkenazi Jewish Sub 3324 A=1.0000 C=0.0000
gnomAD - Genomes East Asian Sub 3128 A=1.0000 C=0.0000
gnomAD - Genomes Other Sub 2150 A=0.9879 C=0.0121
1000Genomes Global Study-wide 5008 A=0.9822 C=0.0178
1000Genomes African Sub 1322 A=0.9349 C=0.0651
1000Genomes East Asian Sub 1008 A=1.0000 C=0.0000
1000Genomes Europe Sub 1006 A=1.0000 C=0.0000
1000Genomes South Asian Sub 978 A=1.000 C=0.000
1000Genomes American Sub 694 A=0.996 C=0.004
Qatari Global Study-wide 216 A=0.991 C=0.009
Ancient Sardinia genome-wide 1240k capture data generation and analysis Global Study-wide 72 A=1.00 C=0.00
SGDP_PRJ Global Study-wide 2 A=0.5 C=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.p13 chr 1 NC_000001.11:g.83044105A>C
GRCh37.p13 chr 1 NC_000001.10:g.83509788A>C
Gene: LINC01362, long intergenic non-protein coding RNA 1362 (plus strand)
Molecule type Change Amino acid[Codon] SO Term
LINC01362 transcript NR_147074.1:n. N/A Intron Variant
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
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 A= C
GRCh38.p13 chr 1 NC_000001.11:g.83044105= NC_000001.11:g.83044105A>C
GRCh37.p13 chr 1 NC_000001.10:g.83509788= NC_000001.10:g.83509788A>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#.

13 SubSNP, 7 Frequency submissions
No Submitter Submission ID Date (Build)
1 PERLEGEN ss23145044 Sep 20, 2004 (123)
2 1000GENOMES ss218491729 Jul 14, 2010 (132)
3 1000GENOMES ss1291668426 Aug 21, 2014 (142)
4 HAMMER_LAB ss1794651186 Sep 08, 2015 (146)
5 WEILL_CORNELL_DGM ss1918568431 Feb 12, 2016 (147)
6 HUMAN_LONGEVITY ss2164128710 Dec 20, 2016 (150)
7 TOPMED ss2326420896 Dec 20, 2016 (150)
8 GNOMAD ss2757360422 Nov 08, 2017 (151)
9 TOPMED ss3081727235 Nov 08, 2017 (151)
10 KHV_HUMAN_GENOMES ss3799446363 Jul 12, 2019 (153)
11 SGDP_PRJ ss3849250134 Apr 25, 2020 (154)
12 EVA ss3984808443 Apr 25, 2021 (155)
13 TOPMED ss4456684180 Apr 25, 2021 (155)
14 1000Genomes NC_000001.10 - 83509788 Oct 11, 2018 (152)
15 gnomAD - Genomes NC_000001.11 - 83044105 Apr 25, 2021 (155)
16 Ancient Sardinia genome-wide 1240k capture data generation and analysis NC_000001.10 - 83509788 Apr 25, 2021 (155)
17 Qatari NC_000001.10 - 83509788 Apr 25, 2020 (154)
18 SGDP_PRJ NC_000001.10 - 83509788 Apr 25, 2020 (154)
19 TopMed NC_000001.11 - 83044105 Apr 25, 2021 (155)
20 ALFA NC_000001.11 - 83044105 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).

Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
2415603, 34370, 610361, 1267114, ss218491729, ss1291668426, ss1794651186, ss1918568431, ss2326420896, ss2757360422, ss3849250134, ss3984808443 NC_000001.10:83509787:A:C NC_000001.11:83044104:A:C (self)
17048133, 12780579, 20290515, 9538997566, ss2164128710, ss3081727235, ss3799446363, ss4456684180 NC_000001.11:83044104:A:C NC_000001.11:83044104:A:C (self)
ss23145044 NT_032977.9:53481705:A:C NC_000001.11:83044104:A: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 rs17109619

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.post629+eb05767