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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.

rs969529703

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr13:29945853-29945860 (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
delT / dupT
Variation Type
Indel Insertion and Deletion
Frequency
dupT=0.00027 (5/18506, ALFA)
dupT=0.00006 (1/16760, 8.3KJPN)
dupT=0.0009 (6/6404, 1000G_30x) (+ 1 more)
dupT=0.0011 (5/4480, Estonian)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
LINC00544 : 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: 20231103111315
Population Group Sample Size Ref Allele Alt Allele Ref HMOZ Alt HMOZ HTRZ HWEP
Total Global 18506 TTTTTTTT=0.99973 TTTTTTT=0.00000, TTTTTTTTT=0.00027 0.99946 0.0 0.00054 0
European Sub 14152 TTTTTTTT=0.99965 TTTTTTT=0.00000, TTTTTTTTT=0.00035 0.999293 0.0 0.000707 0
African Sub 2884 TTTTTTTT=1.0000 TTTTTTT=0.0000, TTTTTTTTT=0.0000 1.0 0.0 0.0 N/A
African Others Sub 112 TTTTTTTT=1.000 TTTTTTT=0.000, TTTTTTTTT=0.000 1.0 0.0 0.0 N/A
African American Sub 2772 TTTTTTTT=1.0000 TTTTTTT=0.0000, TTTTTTTTT=0.0000 1.0 0.0 0.0 N/A
Asian Sub 112 TTTTTTTT=1.000 TTTTTTT=0.000, TTTTTTTTT=0.000 1.0 0.0 0.0 N/A
East Asian Sub 86 TTTTTTTT=1.00 TTTTTTT=0.00, TTTTTTTTT=0.00 1.0 0.0 0.0 N/A
Other Asian Sub 26 TTTTTTTT=1.00 TTTTTTT=0.00, TTTTTTTTT=0.00 1.0 0.0 0.0 N/A
Latin American 1 Sub 146 TTTTTTTT=1.000 TTTTTTT=0.000, TTTTTTTTT=0.000 1.0 0.0 0.0 N/A
Latin American 2 Sub 610 TTTTTTTT=1.000 TTTTTTT=0.000, TTTTTTTTT=0.000 1.0 0.0 0.0 N/A
South Asian Sub 98 TTTTTTTT=1.00 TTTTTTT=0.00, TTTTTTTTT=0.00 1.0 0.0 0.0 N/A
Other Sub 504 TTTTTTTT=1.000 TTTTTTT=0.000, TTTTTTTTT=0.000 1.0 0.0 0.0 N/A


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
Allele Frequency Aggregator Total Global 18506 (T)8=0.99973 delT=0.00000, dupT=0.00027
Allele Frequency Aggregator European Sub 14152 (T)8=0.99965 delT=0.00000, dupT=0.00035
Allele Frequency Aggregator African Sub 2884 (T)8=1.0000 delT=0.0000, dupT=0.0000
Allele Frequency Aggregator Latin American 2 Sub 610 (T)8=1.000 delT=0.000, dupT=0.000
Allele Frequency Aggregator Other Sub 504 (T)8=1.000 delT=0.000, dupT=0.000
Allele Frequency Aggregator Latin American 1 Sub 146 (T)8=1.000 delT=0.000, dupT=0.000
Allele Frequency Aggregator Asian Sub 112 (T)8=1.000 delT=0.000, dupT=0.000
Allele Frequency Aggregator South Asian Sub 98 (T)8=1.00 delT=0.00, dupT=0.00
8.3KJPN JAPANESE Study-wide 16760 -

No frequency provided

dupT=0.00006
1000Genomes_30x Global Study-wide 6404 -

No frequency provided

dupT=0.0009
1000Genomes_30x African Sub 1786 -

No frequency provided

dupT=0.0034
1000Genomes_30x Europe Sub 1266 -

No frequency provided

dupT=0.0000
1000Genomes_30x South Asian Sub 1202 -

No frequency provided

dupT=0.0000
1000Genomes_30x East Asian Sub 1170 -

No frequency provided

dupT=0.0000
1000Genomes_30x American Sub 980 -

No frequency provided

dupT=0.000
Genetic variation in the Estonian population Estonian Study-wide 4480 -

No frequency provided

dupT=0.0011
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 13 NC_000013.11:g.29945860del
GRCh38.p14 chr 13 NC_000013.11:g.29945860dup
GRCh37.p13 chr 13 NC_000013.10:g.30519997del
GRCh37.p13 chr 13 NC_000013.10:g.30519997dup
Gene: LINC00544, long intergenic non-protein coding RNA 544 (plus strand)
Molecule type Change Amino acid[Codon] SO Term
LINC00544 transcript NR_033889.1: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 (T)8= delT dupT
GRCh38.p14 chr 13 NC_000013.11:g.29945853_29945860= NC_000013.11:g.29945860del NC_000013.11:g.29945860dup
GRCh37.p13 chr 13 NC_000013.10:g.30519990_30519997= NC_000013.10:g.30519997del NC_000013.10:g.30519997dup
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, 10 Frequency submissions
No Submitter Submission ID Date (Build)
1 GNOMAD ss2918052623 Jan 10, 2018 (151)
2 SWEGEN ss3010790272 Jan 10, 2018 (151)
3 EGCUT_WGS ss3678050654 Jul 13, 2019 (153)
4 EVA_DECODE ss3695010919 Jul 13, 2019 (153)
5 TOPMED ss4941332189 Apr 26, 2021 (155)
6 TOPMED ss4941332191 Apr 26, 2021 (155)
7 TOMMO_GENOMICS ss5209359275 Apr 26, 2021 (155)
8 1000G_HIGH_COVERAGE ss5293242492 Oct 16, 2022 (156)
9 1000G_HIGH_COVERAGE ss5591943253 Oct 16, 2022 (156)
10 SANFORD_IMAGENETICS ss5654486235 Oct 16, 2022 (156)
11 TOMMO_GENOMICS ss5761052821 Oct 16, 2022 (156)
12 TOMMO_GENOMICS ss5761052822 Oct 16, 2022 (156)
13 EVA ss5924536989 Oct 16, 2022 (156)
14 1000Genomes_30x NC_000013.11 - 29945853 Oct 16, 2022 (156)
15 Genetic variation in the Estonian population NC_000013.10 - 30519990 Oct 12, 2018 (152)
16 gnomAD - Genomes

Submission ignored due to conflicting rows:
Row 426660690 (NC_000013.11:29945852::T 92/138610)
Row 426660691 (NC_000013.11:29945852:T: 9/138610)

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

Submission ignored due to conflicting rows:
Row 426660690 (NC_000013.11:29945852::T 92/138610)
Row 426660691 (NC_000013.11:29945852:T: 9/138610)

- Apr 26, 2021 (155)
18 8.3KJPN NC_000013.10 - 30519990 Apr 26, 2021 (155)
19 14KJPN

Submission ignored due to conflicting rows:
Row 94889925 (NC_000013.11:29945852::T 1/28258)
Row 94889926 (NC_000013.11:29945852:T: 1/28258)

- Oct 16, 2022 (156)
20 14KJPN

Submission ignored due to conflicting rows:
Row 94889925 (NC_000013.11:29945852::T 1/28258)
Row 94889926 (NC_000013.11:29945852:T: 1/28258)

- Oct 16, 2022 (156)
21 TopMed

Submission ignored due to conflicting rows:
Row 156877847 (NC_000013.11:29945852::T 158/264690)
Row 156877849 (NC_000013.11:29945852:T: 13/264690)

- Apr 26, 2021 (155)
22 TopMed

Submission ignored due to conflicting rows:
Row 156877847 (NC_000013.11:29945852::T 158/264690)
Row 156877849 (NC_000013.11:29945852:T: 13/264690)

- Apr 26, 2021 (155)
23 ALFA NC_000013.11 - 29945853 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
ss4941332191, ss5761052822 NC_000013.11:29945852:T: NC_000013.11:29945852:TTTTTTTT:TTT…

NC_000013.11:29945852:TTTTTTTT:TTTTTTT

(self)
11258393808 NC_000013.11:29945852:TTTTTTTT:TTT…

NC_000013.11:29945852:TTTTTTTT:TTTTTTT

NC_000013.11:29945852:TTTTTTTT:TTT…

NC_000013.11:29945852:TTTTTTTT:TTTTTTT

(self)
23788902, 67328582, ss2918052623, ss3010790272, ss3678050654, ss5209359275, ss5654486235 NC_000013.10:30519989::T NC_000013.11:29945852:TTTTTTTT:TTT…

NC_000013.11:29945852:TTTTTTTT:TTTTTTTTT

(self)
79469188, ss3695010919, ss4941332189, ss5293242492, ss5591943253, ss5761052821, ss5924536989 NC_000013.11:29945852::T NC_000013.11:29945852:TTTTTTTT:TTT…

NC_000013.11:29945852:TTTTTTTT:TTTTTTTTT

(self)
11258393808 NC_000013.11:29945852:TTTTTTTT:TTT…

NC_000013.11:29945852:TTTTTTTT:TTTTTTTTT

NC_000013.11:29945852:TTTTTTTT:TTT…

NC_000013.11:29945852:TTTTTTTT:TTTTTTTTT

(self)
Removed from this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Destination RSIDs
ss2359283722 NC_000013.10:30519989:T: NC_000013.11:29945852:TTTTTTTT:TTT…

NC_000013.11:29945852:TTTTTTTT:TTTTTTT

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 rs969529703

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.post820+afb47a3d