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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.

rs142251181

Current Build 155

Released April 9, 2021

Organism
Homo sapiens
Position
chr1:793979-793984 (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
delA / dupA
Variation Type
Indel Insertion and Deletion
Frequency
delA=0.00022 (4/18508, ALFA)
delA=0.09779 (1639/16760, 8.3KJPN)
delA=0.0078 (39/5008, 1000G) (+ 1 more)
delA=0.042 (9/214, Vietnamese)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
LINC01409 : 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.793984del
GRCh38.p13 chr 1 NC_000001.11:g.793984dup
GRCh37.p13 chr 1 NC_000001.10:g.729364del
GRCh37.p13 chr 1 NC_000001.10:g.729364dup
Gene: LINC01409, uncharacterized LINC01409 (plus strand)
Molecule type Change Amino acid[Codon] SO Term
LINC01409 transcript variant X1 XR_002958522.1:n. N/A Intron Variant
LINC01409 transcript variant X5 XR_002958525.1:n. N/A Intron Variant
LINC01409 transcript variant X4 XR_946806.3:n. N/A Intron 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
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 18508 AAAAAA=0.99978 AAAAA=0.00022, AAAAAAA=0.00000
European Sub 14150 AAAAAA=0.99972 AAAAA=0.00028, AAAAAAA=0.00000
African Sub 2898 AAAAAA=1.0000 AAAAA=0.0000, AAAAAAA=0.0000
African Others Sub 114 AAAAAA=1.000 AAAAA=0.000, AAAAAAA=0.000
African American Sub 2784 AAAAAA=1.0000 AAAAA=0.0000, AAAAAAA=0.0000
Asian Sub 106 AAAAAA=1.000 AAAAA=0.000, AAAAAAA=0.000
East Asian Sub 80 AAAAAA=1.00 AAAAA=0.00, AAAAAAA=0.00
Other Asian Sub 26 AAAAAA=1.00 AAAAA=0.00, AAAAAAA=0.00
Latin American 1 Sub 146 AAAAAA=1.000 AAAAA=0.000, AAAAAAA=0.000
Latin American 2 Sub 608 AAAAAA=1.000 AAAAA=0.000, AAAAAAA=0.000
South Asian Sub 98 AAAAAA=1.00 AAAAA=0.00, AAAAAAA=0.00
Other Sub 502 AAAAAA=1.000 AAAAA=0.000, AAAAAAA=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
8.3KJPN JAPANESE Study-wide 16760 (A)6=0.90221 delA=0.09779
1000Genomes Global Study-wide 5008 (A)6=0.9922 delA=0.0078
1000Genomes African Sub 1322 (A)6=1.0000 delA=0.0000
1000Genomes East Asian Sub 1008 (A)6=0.9633 delA=0.0367
1000Genomes Europe Sub 1006 (A)6=0.9990 delA=0.0010
1000Genomes South Asian Sub 978 (A)6=0.999 delA=0.001
1000Genomes American Sub 694 (A)6=1.000 delA=0.000
A Vietnamese Genetic Variation Database Global Study-wide 214 (A)6=0.958 delA=0.042
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)6= delA dupA
GRCh38.p13 chr 1 NC_000001.11:g.793979_793984= NC_000001.11:g.793984del NC_000001.11:g.793984dup
GRCh37.p13 chr 1 NC_000001.10:g.729359_729364= NC_000001.10:g.729364del NC_000001.10:g.729364dup
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 ss325997441 May 09, 2011 (134)
2 1000GENOMES ss498763801 May 04, 2012 (137)
3 LUNTER ss552738971 Apr 25, 2013 (138)
4 SSMP ss663203111 Apr 01, 2015 (144)
5 1000GENOMES ss1367645334 Aug 21, 2014 (142)
6 TOPMED ss2321501587 Dec 20, 2016 (150)
7 GNOMAD ss2750634469 Nov 08, 2017 (151)
8 SWEGEN ss2986148122 Nov 08, 2017 (151)
9 TOPMED ss3066391435 Nov 08, 2017 (151)
10 TOPMED ss3066391436 Nov 08, 2017 (151)
11 KHV_HUMAN_GENOMES ss3798743217 Jul 12, 2019 (153)
12 GNOMAD ss3986922981 Apr 25, 2021 (155)
13 TOPMED ss4436424531 Apr 25, 2021 (155)
14 TOPMED ss4436424532 Apr 25, 2021 (155)
15 TOMMO_GENOMICS ss5142050140 Apr 25, 2021 (155)
16 1000Genomes NC_000001.10 - 729359 Oct 11, 2018 (152)
17 gnomAD - Genomes

Submission ignored due to conflicting rows:
Row 56701 (NC_000001.11:793978::A 1/140194)
Row 56702 (NC_000001.11:793978:A: 162/140192)

- Apr 25, 2021 (155)
18 gnomAD - Genomes

Submission ignored due to conflicting rows:
Row 56701 (NC_000001.11:793978::A 1/140194)
Row 56702 (NC_000001.11:793978:A: 162/140192)

- Apr 25, 2021 (155)
19 8.3KJPN NC_000001.10 - 729359 Apr 25, 2021 (155)
20 TopMed

Submission ignored due to conflicting rows:
Row 11903 (NC_000001.11:793978::A 1/125568)
Row 11904 (NC_000001.11:793978:A: 245/125568)

- Oct 11, 2018 (152)
21 TopMed

Submission ignored due to conflicting rows:
Row 30866 (NC_000001.11:793978::A 1/264690)
Row 30867 (NC_000001.11:793978:A: 312/264690)

- Apr 25, 2021 (155)
22 TopMed

Submission ignored due to conflicting rows:
Row 30866 (NC_000001.11:793978::A 1/264690)
Row 30867 (NC_000001.11:793978:A: 312/264690)

- Apr 25, 2021 (155)
23 A Vietnamese Genetic Variation Database NC_000001.10 - 729359 Jul 12, 2019 (153)
24 ALFA NC_000001.11 - 793979 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
ss325997441, ss552738971 NC_000001.9:719221:A: NC_000001.11:793978:AAAAAA:AAAAA (self)
2948, 19447, 28, ss498763801, ss663203111, ss1367645334, ss2321501587, ss2750634469, ss2986148122, ss5142050140 NC_000001.10:729358:A: NC_000001.11:793978:AAAAAA:AAAAA (self)
ss3066391436, ss3798743217, ss4436424532 NC_000001.11:793978:A: NC_000001.11:793978:AAAAAA:AAAAA (self)
11947785137 NC_000001.11:793978:AAAAAA:AAAAA NC_000001.11:793978:AAAAAA:AAAAA (self)
ss3066391435, ss3986922981, ss4436424531 NC_000001.11:793978::A NC_000001.11:793978:AAAAAA:AAAAAAA (self)
11947785137 NC_000001.11:793978:AAAAAA:AAAAAAA NC_000001.11:793978:AAAAAA:AAAAAAA (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 rs142251181

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