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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.

rs138660747

Current Build 155

Released April 9, 2021

Organism
Homo sapiens
Position
chr1:778897 (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>A
Variation Type
SNV Single Nucleotide Variation
Frequency
A=0.005146 (1362/264690, TOPMED)
A=0.004769 (669/140284, GnomAD)
A=0.00556 (105/18890, ALFA) (+ 7 more)
A=0.0012 (6/5008, 1000G)
A=0.0099 (38/3854, ALSPAC)
A=0.0062 (23/3708, TWINSUK)
A=0.009 (9/998, GoNL)
A=0.03 (1/40, GENOME_DK)
C=0.5 (1/2, SGDP_PRJ)
A=0.5 (1/2, SGDP_PRJ)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
LINC01409 : Non Coding Transcript Variant
LOC100288069 : 2KB Upstream 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.778897C>A
GRCh37.p13 chr 1 NC_000001.10:g.714277C>A
Gene: LOC100288069, uncharacterized LOC100288069 (minus strand) : 2KB Upstream Variant
Molecule type Change Amino acid[Codon] SO Term
LOC100288069 transcript NR_168328.1:n. N/A Upstream Transcript Variant
Gene: LINC01409, uncharacterized LINC01409 (plus strand)
Molecule type Change Amino acid[Codon] SO Term
LINC01409 transcript variant X4 XR_946806.3:n.156C>A N/A Non Coding Transcript Variant
LINC01409 transcript variant X5 XR_002958525.1:n.89C>A N/A Non Coding Transcript Variant
LINC01409 transcript variant X1 XR_002958522.1:n. N/A Genic Upstream Transcript Variant
LINC01409 transcript variant X2 XR_002958523.1:n. N/A Genic Upstream Transcript Variant
LINC01409 transcript variant X3 XR_002958524.1:n. 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

ALFA Allele Frequency (New)
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 18890 C=0.99444 A=0.00556
European Sub 14286 C=0.99370 A=0.00630
African Sub 2946 C=0.9983 A=0.0017
African Others Sub 114 C=1.000 A=0.000
African American Sub 2832 C=0.9982 A=0.0018
Asian Sub 112 C=1.000 A=0.000
East Asian Sub 86 C=1.00 A=0.00
Other Asian Sub 26 C=1.00 A=0.00
Latin American 1 Sub 146 C=0.979 A=0.021
Latin American 2 Sub 610 C=0.995 A=0.005
South Asian Sub 98 C=1.00 A=0.00
Other Sub 692 C=0.994 A=0.006


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=0.994854 A=0.005146
gnomAD - Genomes Global Study-wide 140284 C=0.995231 A=0.004769
gnomAD - Genomes European Sub 75952 C=0.99314 A=0.00686
gnomAD - Genomes African Sub 42054 C=0.99817 A=0.00183
gnomAD - Genomes American Sub 13668 C=0.99671 A=0.00329
gnomAD - Genomes Ashkenazi Jewish Sub 3324 C=0.9982 A=0.0018
gnomAD - Genomes East Asian Sub 3132 C=1.0000 A=0.0000
gnomAD - Genomes Other Sub 2154 C=0.9907 A=0.0093
1000Genomes Global Study-wide 5008 C=0.9988 A=0.0012
1000Genomes African Sub 1322 C=1.0000 A=0.0000
1000Genomes East Asian Sub 1008 C=1.0000 A=0.0000
1000Genomes Europe Sub 1006 C=0.9970 A=0.0030
1000Genomes South Asian Sub 978 C=0.998 A=0.002
1000Genomes American Sub 694 C=0.999 A=0.001
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 C=0.9901 A=0.0099
UK 10K study - Twins TWIN COHORT Study-wide 3708 C=0.9938 A=0.0062
Genome of the Netherlands Release 5 Genome of the Netherlands Study-wide 998 C=0.991 A=0.009
The Danish reference pan genome Danish Study-wide 40 C=0.97 A=0.03
SGDP_PRJ Global Study-wide 2 C=0.5 A=0.5
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= A
GRCh38.p13 chr 1 NC_000001.11:g.778897= NC_000001.11:g.778897C>A
GRCh37.p13 chr 1 NC_000001.10:g.714277= NC_000001.10:g.714277C>A
LINC01409 transcript variant X4 XR_946806.3:n.156= XR_946806.3:n.156C>A
LINC01409 transcript variant X5 XR_002958525.1:n.89= XR_002958525.1:n.89C>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#.

15 SubSNP, 9 Frequency submissions
No Submitter Submission ID Date (Build)
1 1000GENOMES ss328357065 May 09, 2011 (134)
2 EVA-GONL ss974769040 Aug 21, 2014 (142)
3 1000GENOMES ss1289337888 Aug 21, 2014 (142)
4 EVA_GENOME_DK ss1573851053 Apr 01, 2015 (144)
5 EVA_DECODE ss1584129324 Apr 01, 2015 (144)
6 EVA_UK10K_ALSPAC ss1599378226 Apr 01, 2015 (144)
7 EVA_UK10K_TWINSUK ss1642372259 Apr 01, 2015 (144)
8 JJLAB ss2019498259 Sep 14, 2016 (149)
9 TOPMED ss2321500909 Dec 20, 2016 (150)
10 GNOMAD ss2750632782 Nov 08, 2017 (151)
11 SWEGEN ss2986147680 Nov 08, 2017 (151)
12 TOPMED ss3066388263 Nov 08, 2017 (151)
13 EVA_DECODE ss3685991604 Jul 12, 2019 (153)
14 SGDP_PRJ ss3847993771 Apr 25, 2020 (154)
15 TOPMED ss4436421674 Apr 25, 2021 (155)
16 1000Genomes NC_000001.10 - 714277 Oct 11, 2018 (152)
17 The Avon Longitudinal Study of Parents and Children NC_000001.10 - 714277 Oct 11, 2018 (152)
18 The Danish reference pan genome NC_000001.10 - 714277 Apr 25, 2020 (154)
19 gnomAD - Genomes NC_000001.11 - 778897 Apr 25, 2021 (155)
20 Genome of the Netherlands Release 5 NC_000001.10 - 714277 Apr 25, 2020 (154)
21 SGDP_PRJ NC_000001.10 - 714277 Apr 25, 2020 (154)
22 TopMed NC_000001.11 - 778897 Apr 25, 2021 (155)
23 UK 10K study - Twins NC_000001.10 - 714277 Oct 11, 2018 (152)
24 ALFA NC_000001.11 - 778897 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
ss1584129324 NC_000001.9:704139:C:A NC_000001.11:778896:C:A (self)
2549, 67, 1358287, 160, 10751, 67, ss328357065, ss974769040, ss1289337888, ss1573851053, ss1599378226, ss1642372259, ss2019498259, ss2321500909, ss2750632782, ss2986147680, ss3847993771 NC_000001.10:714276:C:A NC_000001.11:778896:C:A (self)
53227, 10270, 28009, 11870501181, ss3066388263, ss3685991604, ss4436421674 NC_000001.11:778896:C:A NC_000001.11:778896:C: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 rs138660747

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