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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.

rs371583549

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr1:786345-786348 (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
dupT
Variation Type
Indel Insertion and Deletion
Frequency
dupT=0.001213 (321/264690, TOPMED)
dupT=0.001184 (166/140186, GnomAD)
dupT=0.002687 (363/135098, GnomAD_exome) (+ 7 more)
dupT=0.00053 (18/33904, ALFA)
dupT=0.09923 (2804/28258, 14KJPN)
dupT=0.09833 (1648/16760, 8.3KJPN)
dupT=0.00198 (26/13134, ExAC)
dupT=0.0066 (42/6404, 1000G_30x)
dupT=0.0080 (40/5008, 1000G)
dupT=0.038 (8/210, Vietnamese)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
LINC01409 : Non Coding Transcript 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 33904 TTTT=0.99947 TTTTT=0.00053
European Sub 26360 TTTT=0.99981 TTTTT=0.00019
African Sub 3492 TTTT=1.0000 TTTTT=0.0000
African Others Sub 122 TTTT=1.000 TTTTT=0.000
African American Sub 3370 TTTT=1.0000 TTTTT=0.0000
Asian Sub 168 TTTT=0.970 TTTTT=0.030
East Asian Sub 112 TTTT=0.955 TTTTT=0.045
Other Asian Sub 56 TTTT=1.00 TTTTT=0.00
Latin American 1 Sub 146 TTTT=1.000 TTTTT=0.000
Latin American 2 Sub 610 TTTT=0.998 TTTTT=0.002
South Asian Sub 98 TTTT=1.00 TTTTT=0.00
Other Sub 3030 TTTT=0.9977 TTTTT=0.0023


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 -

No frequency provided

dupT=0.001213
gnomAD - Genomes Global Study-wide 140186 -

No frequency provided

dupT=0.001184
gnomAD - Genomes European Sub 75920 -

No frequency provided

dupT=0.00066
gnomAD - Genomes African Sub 42034 -

No frequency provided

dupT=0.00007
gnomAD - Genomes American Sub 13636 -

No frequency provided

dupT=0.00037
gnomAD - Genomes Ashkenazi Jewish Sub 3322 -

No frequency provided

dupT=0.0000
gnomAD - Genomes East Asian Sub 3124 -

No frequency provided

dupT=0.0320
gnomAD - Genomes Other Sub 2150 -

No frequency provided

dupT=0.0037
gnomAD - Exomes Global Study-wide 135098 -

No frequency provided

dupT=0.002687
gnomAD - Exomes European Sub 59234 -

No frequency provided

dupT=0.00037
gnomAD - Exomes Asian Sub 32740 -

No frequency provided

dupT=0.01002
gnomAD - Exomes American Sub 24328 -

No frequency provided

dupT=0.00000
gnomAD - Exomes Ashkenazi Jewish Sub 8246 -

No frequency provided

dupT=0.0000
gnomAD - Exomes African Sub 6414 -

No frequency provided

dupT=0.0003
gnomAD - Exomes Other Sub 4136 -

No frequency provided

dupT=0.0027
Allele Frequency Aggregator Total Global 33904 (T)4=0.99947 dupT=0.00053
Allele Frequency Aggregator European Sub 26360 (T)4=0.99981 dupT=0.00019
Allele Frequency Aggregator African Sub 3492 (T)4=1.0000 dupT=0.0000
Allele Frequency Aggregator Other Sub 3030 (T)4=0.9977 dupT=0.0023
Allele Frequency Aggregator Latin American 2 Sub 610 (T)4=0.998 dupT=0.002
Allele Frequency Aggregator Asian Sub 168 (T)4=0.970 dupT=0.030
Allele Frequency Aggregator Latin American 1 Sub 146 (T)4=1.000 dupT=0.000
Allele Frequency Aggregator South Asian Sub 98 (T)4=1.00 dupT=0.00
14KJPN JAPANESE Study-wide 28258 -

No frequency provided

dupT=0.09923
8.3KJPN JAPANESE Study-wide 16760 -

No frequency provided

dupT=0.09833
ExAC Global Study-wide 13134 -

No frequency provided

dupT=0.00198
ExAC Asian Sub 7818 -

No frequency provided

dupT=0.0029
ExAC Europe Sub 4416 -

No frequency provided

dupT=0.0007
ExAC African Sub 560 -

No frequency provided

dupT=0.000
ExAC American Sub 186 -

No frequency provided

dupT=0.000
ExAC Other Sub 154 -

No frequency provided

dupT=0.000
1000Genomes_30x Global Study-wide 6404 -

No frequency provided

dupT=0.0066
1000Genomes_30x African Sub 1786 -

No frequency provided

dupT=0.0000
1000Genomes_30x Europe Sub 1266 -

No frequency provided

dupT=0.0008
1000Genomes_30x South Asian Sub 1202 -

No frequency provided

dupT=0.0008
1000Genomes_30x East Asian Sub 1170 -

No frequency provided

dupT=0.0342
1000Genomes_30x American Sub 980 -

No frequency provided

dupT=0.000
1000Genomes Global Study-wide 5008 -

No frequency provided

dupT=0.0080
1000Genomes African Sub 1322 -

No frequency provided

dupT=0.0000
1000Genomes East Asian Sub 1008 -

No frequency provided

dupT=0.0377
1000Genomes Europe Sub 1006 -

No frequency provided

dupT=0.0010
1000Genomes South Asian Sub 978 -

No frequency provided

dupT=0.001
1000Genomes American Sub 694 -

No frequency provided

dupT=0.000
A Vietnamese Genetic Variation Database Global Study-wide 210 -

No frequency provided

dupT=0.038
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 1 NC_000001.11:g.786348dup
GRCh37.p13 chr 1 NC_000001.10:g.721728dup
Gene: LINC01409, uncharacterized LINC01409 (plus strand)
Molecule type Change Amino acid[Codon] SO Term
LINC01409 transcript variant X1 XR_007065319.1:n.4747dup N/A Non Coding Transcript Variant
LINC01409 transcript variant X2 XR_007065320.1:n.2280dup N/A Non Coding 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
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 (T)4= dupT
GRCh38.p14 chr 1 NC_000001.11:g.786345_786348= NC_000001.11:g.786348dup
GRCh37.p13 chr 1 NC_000001.10:g.721725_721728= NC_000001.10:g.721728dup
LINC01409 transcript variant X1 XR_007065319.1:n.4744_4747= XR_007065319.1:n.4747dup
LINC01409 transcript variant X2 XR_007065320.1:n.2277_2280= XR_007065320.1:n.2280dup
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#.

19 SubSNP, 10 Frequency submissions
No Submitter Submission ID Date (Build)
1 LUNTER ss552738966 Apr 25, 2013 (138)
2 1000GENOMES ss1367645313 Aug 21, 2014 (142)
3 EVA_EXAC ss1711595262 Apr 01, 2015 (144)
4 GNOMAD ss2730986529 Nov 08, 2017 (151)
5 GNOMAD ss2746169222 Nov 08, 2017 (151)
6 GNOMAD ss2750633364 Nov 08, 2017 (151)
7 AFFY ss2984840979 Nov 08, 2017 (151)
8 SWEGEN ss2986147781 Nov 08, 2017 (151)
9 ILLUMINA ss3653614730 Oct 11, 2018 (152)
10 KHV_HUMAN_GENOMES ss3798743120 Jul 12, 2019 (153)
11 TOPMED ss4436423325 Apr 25, 2021 (155)
12 TOMMO_GENOMICS ss5142049551 Apr 25, 2021 (155)
13 EVA ss5236862232 Apr 25, 2021 (155)
14 1000G_HIGH_COVERAGE ss5240861490 Oct 12, 2022 (156)
15 HUGCELL_USP ss5442111669 Oct 12, 2022 (156)
16 1000G_HIGH_COVERAGE ss5512485802 Oct 12, 2022 (156)
17 SANFORD_IMAGENETICS ss5624747931 Oct 12, 2022 (156)
18 TOMMO_GENOMICS ss5666187877 Oct 12, 2022 (156)
19 YY_MCH ss5800243151 Oct 12, 2022 (156)
20 1000Genomes NC_000001.10 - 721725 Oct 11, 2018 (152)
21 1000Genomes_30x NC_000001.11 - 786345 Oct 12, 2022 (156)
22 ExAC NC_000001.10 - 721725 Oct 11, 2018 (152)
23 gnomAD - Genomes NC_000001.11 - 786345 Apr 25, 2021 (155)
24 gnomAD - Exomes NC_000001.10 - 721725 Jul 12, 2019 (153)
25 8.3KJPN NC_000001.10 - 721725 Apr 25, 2021 (155)
26 14KJPN NC_000001.11 - 786345 Oct 12, 2022 (156)
27 TopMed NC_000001.11 - 786345 Apr 25, 2021 (155)
28 A Vietnamese Genetic Variation Database NC_000001.10 - 721725 Jul 12, 2019 (153)
29 ALFA NC_000001.11 - 786345 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
ss552738966 NC_000001.9:711587::T NC_000001.11:786344:TTTT:TTTTT (self)
2714, 4390218, 897, 18858, 26, ss1367645313, ss1711595262, ss2730986529, ss2746169222, ss2750633364, ss2984840979, ss2986147781, ss3653614730, ss5142049551, ss5624747931 NC_000001.10:721724::T NC_000001.11:786344:TTTT:TTTTT (self)
11737, 54509, 24981, 29660, ss3798743120, ss4436423325, ss5236862232, ss5240861490, ss5442111669, ss5512485802, ss5666187877, ss5800243151 NC_000001.11:786344::T NC_000001.11:786344:TTTT:TTTTT (self)
12672510069 NC_000001.11:786344:TTTT:TTTTT NC_000001.11:786344:TTTT:TTTTT (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 rs371583549

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