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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.

rs28729284

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr3:18524 (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
C>G / C>T
Variation Type
SNV Single Nucleotide Variation
Frequency
G=0.008395 (2222/264690, TOPMED)
G=0.00000 (0/14236, ALFA)
T=0.00000 (0/14236, ALFA) (+ 5 more)
G=0.0083 (53/6404, 1000G_30x)
G=0.0088 (44/5008, 1000G)
G=0.005 (1/216, Qatari)
C=0.5 (1/2, SGDP_PRJ)
G=0.5 (1/2, SGDP_PRJ)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
LINC01986 : 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 14236 C=1.00000 G=0.00000, T=0.00000
European Sub 9822 C=1.0000 G=0.0000, T=0.0000
African Sub 2782 C=1.0000 G=0.0000, T=0.0000
African Others Sub 108 C=1.000 G=0.000, T=0.000
African American Sub 2674 C=1.0000 G=0.0000, T=0.0000
Asian Sub 112 C=1.000 G=0.000, T=0.000
East Asian Sub 86 C=1.00 G=0.00, T=0.00
Other Asian Sub 26 C=1.00 G=0.00, T=0.00
Latin American 1 Sub 142 C=1.000 G=0.000, T=0.000
Latin American 2 Sub 610 C=1.000 G=0.000, T=0.000
South Asian Sub 98 C=1.00 G=0.00, T=0.00
Other Sub 670 C=1.000 G=0.000, T=0.000


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 C=0.991605 G=0.008395
Allele Frequency Aggregator Total Global 14236 C=1.00000 G=0.00000, T=0.00000
Allele Frequency Aggregator European Sub 9822 C=1.0000 G=0.0000, T=0.0000
Allele Frequency Aggregator African Sub 2782 C=1.0000 G=0.0000, T=0.0000
Allele Frequency Aggregator Other Sub 670 C=1.000 G=0.000, T=0.000
Allele Frequency Aggregator Latin American 2 Sub 610 C=1.000 G=0.000, T=0.000
Allele Frequency Aggregator Latin American 1 Sub 142 C=1.000 G=0.000, T=0.000
Allele Frequency Aggregator Asian Sub 112 C=1.000 G=0.000, T=0.000
Allele Frequency Aggregator South Asian Sub 98 C=1.00 G=0.00, T=0.00
1000Genomes_30x Global Study-wide 6404 C=0.9917 G=0.0083
1000Genomes_30x African Sub 1786 C=0.9703 G=0.0297
1000Genomes_30x Europe Sub 1266 C=1.0000 G=0.0000
1000Genomes_30x South Asian Sub 1202 C=1.0000 G=0.0000
1000Genomes_30x East Asian Sub 1170 C=1.0000 G=0.0000
1000Genomes_30x American Sub 980 C=1.000 G=0.000
1000Genomes Global Study-wide 5008 C=0.9912 G=0.0088
1000Genomes African Sub 1322 C=0.9667 G=0.0333
1000Genomes East Asian Sub 1008 C=1.0000 G=0.0000
1000Genomes Europe Sub 1006 C=1.0000 G=0.0000
1000Genomes South Asian Sub 978 C=1.000 G=0.000
1000Genomes American Sub 694 C=1.000 G=0.000
Qatari Global Study-wide 216 C=0.995 G=0.005
SGDP_PRJ Global Study-wide 2 C=0.5 G=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 3 NC_000003.12:g.18524C>G
GRCh38.p14 chr 3 NC_000003.12:g.18524C>T
GRCh37.p13 chr 3 NC_000003.11:g.60202C>G
GRCh37.p13 chr 3 NC_000003.11:g.60202C>T
Gene: LINC01986, long intergenic non-protein coding RNA 1986 (plus strand)
Molecule type Change Amino acid[Codon] SO Term
LINC01986 transcript NR_110824.1: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 C= G T
GRCh38.p14 chr 3 NC_000003.12:g.18524= NC_000003.12:g.18524C>G NC_000003.12:g.18524C>T
GRCh37.p13 chr 3 NC_000003.11:g.60202= NC_000003.11:g.60202C>G NC_000003.11:g.60202C>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#.

15 SubSNP, 8 Frequency submissions
No Submitter Submission ID Date (Build)
1 SSAHASNP ss35519661 May 24, 2005 (125)
2 BUSHMAN ss201990170 Jul 04, 2010 (132)
3 1000GENOMES ss330430897 May 09, 2011 (134)
4 1000GENOMES ss1302408211 Aug 21, 2014 (142)
5 WEILL_CORNELL_DGM ss1921415459 Feb 12, 2016 (147)
6 JJLAB ss2021256216 Sep 14, 2016 (149)
7 GNOMAD ss2788465708 Nov 08, 2017 (151)
8 KHV_HUMAN_GENOMES ss3802685187 Jul 13, 2019 (153)
9 SGDP_PRJ ss3855010918 Apr 25, 2020 (154)
10 TOPMED ss4551018208 Apr 26, 2021 (155)
11 1000G_HIGH_COVERAGE ss5252706744 Oct 13, 2022 (156)
12 EVA ss5337266999 Oct 13, 2022 (156)
13 1000G_HIGH_COVERAGE ss5530370893 Oct 13, 2022 (156)
14 SANFORD_IMAGENETICS ss5631338367 Oct 13, 2022 (156)
15 EVA ss5959593883 Oct 13, 2022 (156)
16 1000Genomes NC_000003.11 - 60202 Oct 11, 2018 (152)
17 1000Genomes_30x NC_000003.12 - 18524 Oct 13, 2022 (156)
18 gnomAD - Genomes

Submission ignored due to conflicting rows:
Row 96340275 (NC_000003.12:18523:C:G 1104/136994)
Row 96340276 (NC_000003.12:18523:C:T 1/137004)

- Apr 26, 2021 (155)
19 gnomAD - Genomes

Submission ignored due to conflicting rows:
Row 96340275 (NC_000003.12:18523:C:G 1104/136994)
Row 96340276 (NC_000003.12:18523:C:T 1/137004)

- Apr 26, 2021 (155)
20 Qatari NC_000003.11 - 60202 Apr 25, 2020 (154)
21 SGDP_PRJ NC_000003.11 - 60202 Apr 25, 2020 (154)
22 TopMed NC_000003.12 - 18524 Apr 26, 2021 (155)
23 ALFA NC_000003.12 - 18524 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
ss35519661 NC_000003.9:35201:C:G NC_000003.12:18523:C:G (self)
ss201990170 NC_000003.10:35201:C:G NC_000003.12:18523:C:G (self)
13540560, 3457389, 7027898, ss330430897, ss1302408211, ss1921415459, ss2021256216, ss2788465708, ss3855010918, ss5337266999, ss5631338367, ss5959593883 NC_000003.11:60201:C:G NC_000003.12:18523:C:G (self)
17896828, 388395763, 2486958362, ss3802685187, ss4551018208, ss5252706744, ss5530370893 NC_000003.12:18523:C:G NC_000003.12:18523:C:G (self)
2486958362 NC_000003.12:18523:C:T NC_000003.12:18523: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 rs28729284

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