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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.

rs747634485

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr10:106172764-106172768 (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
delTATA / delTA / dupTA
Variation Type
Indel Insertion and Deletion
Frequency
delTATA=0.00050 (14/28256, 14KJPN)
delTATA=0.00024 (3/12488, 8.3KJPN)
delTATA=0.0000 (0/8196, ALFA) (+ 5 more)
delTA=0.0000 (0/8196, ALFA)
dupTA=0.0000 (0/8196, ALFA)
delTATA=0.3954 (1524/3854, ALSPAC)
delTATA=0.3679 (1364/3708, TWINSUK)
delTATA=0.0012 (2/1626, Korea1K)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
LINC02624 : 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 8196 ATATA=1.0000 A=0.0000, ATA=0.0000, ATATATA=0.0000 1.0 0.0 0.0 N/A
European Sub 4656 ATATA=1.0000 A=0.0000, ATA=0.0000, ATATATA=0.0000 1.0 0.0 0.0 N/A
African Sub 2546 ATATA=1.0000 A=0.0000, ATA=0.0000, ATATATA=0.0000 1.0 0.0 0.0 N/A
African Others Sub 106 ATATA=1.000 A=0.000, ATA=0.000, ATATATA=0.000 1.0 0.0 0.0 N/A
African American Sub 2440 ATATA=1.0000 A=0.0000, ATA=0.0000, ATATATA=0.0000 1.0 0.0 0.0 N/A
Asian Sub 72 ATATA=1.00 A=0.00, ATA=0.00, ATATATA=0.00 1.0 0.0 0.0 N/A
East Asian Sub 54 ATATA=1.00 A=0.00, ATA=0.00, ATATATA=0.00 1.0 0.0 0.0 N/A
Other Asian Sub 18 ATATA=1.00 A=0.00, ATA=0.00, ATATATA=0.00 1.0 0.0 0.0 N/A
Latin American 1 Sub 92 ATATA=1.00 A=0.00, ATA=0.00, ATATATA=0.00 1.0 0.0 0.0 N/A
Latin American 2 Sub 418 ATATA=1.000 A=0.000, ATA=0.000, ATATATA=0.000 1.0 0.0 0.0 N/A
South Asian Sub 66 ATATA=1.00 A=0.00, ATA=0.00, ATATATA=0.00 1.0 0.0 0.0 N/A
Other Sub 346 ATATA=1.000 A=0.000, ATA=0.000, ATATATA=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
14KJPN JAPANESE Study-wide 28256 ATATA=0.99950 delTATA=0.00050
8.3KJPN JAPANESE Study-wide 12488 ATATA=0.99976 delTATA=0.00024
Allele Frequency Aggregator Total Global 8196 ATATA=1.0000 delTATA=0.0000, delTA=0.0000, dupTA=0.0000
Allele Frequency Aggregator European Sub 4656 ATATA=1.0000 delTATA=0.0000, delTA=0.0000, dupTA=0.0000
Allele Frequency Aggregator African Sub 2546 ATATA=1.0000 delTATA=0.0000, delTA=0.0000, dupTA=0.0000
Allele Frequency Aggregator Latin American 2 Sub 418 ATATA=1.000 delTATA=0.000, delTA=0.000, dupTA=0.000
Allele Frequency Aggregator Other Sub 346 ATATA=1.000 delTATA=0.000, delTA=0.000, dupTA=0.000
Allele Frequency Aggregator Latin American 1 Sub 92 ATATA=1.00 delTATA=0.00, delTA=0.00, dupTA=0.00
Allele Frequency Aggregator Asian Sub 72 ATATA=1.00 delTATA=0.00, delTA=0.00, dupTA=0.00
Allele Frequency Aggregator South Asian Sub 66 ATATA=1.00 delTATA=0.00, delTA=0.00, dupTA=0.00
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 ATATA=0.6046 delTATA=0.3954
UK 10K study - Twins TWIN COHORT Study-wide 3708 ATATA=0.6321 delTATA=0.3679
Korean Genome Project KOREAN Study-wide 1626 ATATA=0.9988 delTATA=0.0012
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 10 NC_000010.11:g.106172765_106172768del
GRCh38.p14 chr 10 NC_000010.11:g.106172765TA[1]
GRCh38.p14 chr 10 NC_000010.11:g.106172765TA[3]
GRCh37.p13 chr 10 NC_000010.10:g.107932523_107932526del
GRCh37.p13 chr 10 NC_000010.10:g.107932523TA[1]
GRCh37.p13 chr 10 NC_000010.10:g.107932523TA[3]
Gene: LINC02624, long intergenic non-protein coding RNA 2624 (plus strand)
Molecule type Change Amino acid[Codon] SO Term
LINC02624 transcript variant 2 NR_134330.1:n. N/A Intron Variant
LINC02624 transcript variant 1 NR_134329.1:n. N/A Genic Downstream Transcript Variant
LINC02624 transcript variant 3 NR_134331.1:n. N/A Genic Downstream 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 ATATA= delTATA delTA dupTA
GRCh38.p14 chr 10 NC_000010.11:g.106172764_106172768= NC_000010.11:g.106172765_106172768del NC_000010.11:g.106172765TA[1] NC_000010.11:g.106172765TA[3]
GRCh37.p13 chr 10 NC_000010.10:g.107932522_107932526= NC_000010.10:g.107932523_107932526del NC_000010.10:g.107932523TA[1] NC_000010.10:g.107932523TA[3]
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#.

10 SubSNP, 9 Frequency submissions
No Submitter Submission ID Date (Build)
1 EVA_UK10K_ALSPAC ss1706887055 Apr 01, 2015 (144)
2 EVA_UK10K_TWINSUK ss1706887177 Apr 01, 2015 (144)
3 SWEGEN ss3007093347 Nov 08, 2017 (151)
4 KOGIC ss3968615336 Apr 26, 2020 (154)
5 GNOMAD ss4225018115 Apr 26, 2021 (155)
6 GNOMAD ss4225018118 Apr 26, 2021 (155)
7 GNOMAD ss4225018119 Apr 26, 2021 (155)
8 TOMMO_GENOMICS ss5199327414 Apr 26, 2021 (155)
9 SANFORD_IMAGENETICS ss5650029373 Oct 13, 2022 (156)
10 TOMMO_GENOMICS ss5745655079 Oct 13, 2022 (156)
11 The Avon Longitudinal Study of Parents and Children NC_000010.10 - 107932522 Oct 12, 2018 (152)
12 gnomAD - Genomes

Submission ignored due to conflicting rows:
Row 363013896 (NC_000010.11:106172763::AT 2/31528)
Row 363013899 (NC_000010.11:106172763:AT: 34/31528)
Row 363013900 (NC_000010.11:106172763:ATAT: 76/31518)

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

Submission ignored due to conflicting rows:
Row 363013896 (NC_000010.11:106172763::AT 2/31528)
Row 363013899 (NC_000010.11:106172763:AT: 34/31528)
Row 363013900 (NC_000010.11:106172763:ATAT: 76/31518)

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

Submission ignored due to conflicting rows:
Row 363013896 (NC_000010.11:106172763::AT 2/31528)
Row 363013899 (NC_000010.11:106172763:AT: 34/31528)
Row 363013900 (NC_000010.11:106172763:ATAT: 76/31518)

- Apr 26, 2021 (155)
15 Korean Genome Project NC_000010.11 - 106172764 Apr 26, 2020 (154)
16 8.3KJPN NC_000010.10 - 107932522 Apr 26, 2021 (155)
17 14KJPN NC_000010.11 - 106172764 Oct 13, 2022 (156)
18 UK 10K study - Twins NC_000010.10 - 107932522 Oct 12, 2018 (152)
19 ALFA NC_000010.11 - 106172764 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
28526634, 57296721, 28526634, ss1706887055, ss1706887177, ss3007093347, ss5199327414, ss5650029373 NC_000010.10:107932521:ATAT: NC_000010.11:106172763:ATATA:A (self)
24993337, 79492183, ss3968615336, ss4225018119, ss5745655079 NC_000010.11:106172763:ATAT: NC_000010.11:106172763:ATATA:A (self)
1798505968 NC_000010.11:106172763:ATATA:A NC_000010.11:106172763:ATATA:A (self)
ss4225018118 NC_000010.11:106172763:AT: NC_000010.11:106172763:ATATA:ATA (self)
1798505968 NC_000010.11:106172763:ATATA:ATA NC_000010.11:106172763:ATATA:ATA (self)
ss4225018115 NC_000010.11:106172763::AT NC_000010.11:106172763:ATATA:ATATA…

NC_000010.11:106172763:ATATA:ATATATA

(self)
1798505968 NC_000010.11:106172763:ATATA:ATATA…

NC_000010.11:106172763:ATATA:ATATATA

NC_000010.11:106172763:ATATA:ATATA…

NC_000010.11:106172763:ATATA:ATATATA

(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 rs747634485

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