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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.

rs1217212087

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr7:66839115-66839123 (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
delATAT / delAT / dupAT
Variation Type
Indel Insertion and Deletion
Frequency
delATAT=0.000004 (1/264690, TOPMED)
delAT=0.00007 (2/28250, 14KJPN)
delAT=0.00054 (10/18482, ALFA) (+ 2 more)
delAT=0.00018 (3/16736, 8.3KJPN)
delAT=0.0005 (1/1820, Korea1K)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
GTF2IRD1P1 : 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 18482 TATATATAT=0.99946 TATAT=0.00000, TATATAT=0.00054, TATATATATAT=0.00000 0.998917 0.0 0.001083 0
European Sub 14120 TATATATAT=0.99929 TATAT=0.00000, TATATAT=0.00071, TATATATATAT=0.00000 0.998583 0.0 0.001417 0
African Sub 2894 TATATATAT=1.0000 TATAT=0.0000, TATATAT=0.0000, TATATATATAT=0.0000 1.0 0.0 0.0 N/A
African Others Sub 114 TATATATAT=1.000 TATAT=0.000, TATATAT=0.000, TATATATATAT=0.000 1.0 0.0 0.0 N/A
African American Sub 2780 TATATATAT=1.0000 TATAT=0.0000, TATATAT=0.0000, TATATATATAT=0.0000 1.0 0.0 0.0 N/A
Asian Sub 112 TATATATAT=1.000 TATAT=0.000, TATATAT=0.000, TATATATATAT=0.000 1.0 0.0 0.0 N/A
East Asian Sub 86 TATATATAT=1.00 TATAT=0.00, TATATAT=0.00, TATATATATAT=0.00 1.0 0.0 0.0 N/A
Other Asian Sub 26 TATATATAT=1.00 TATAT=0.00, TATATAT=0.00, TATATATATAT=0.00 1.0 0.0 0.0 N/A
Latin American 1 Sub 146 TATATATAT=1.000 TATAT=0.000, TATATAT=0.000, TATATATATAT=0.000 1.0 0.0 0.0 N/A
Latin American 2 Sub 610 TATATATAT=1.000 TATAT=0.000, TATATAT=0.000, TATATATATAT=0.000 1.0 0.0 0.0 N/A
South Asian Sub 98 TATATATAT=1.00 TATAT=0.00, TATATAT=0.00, TATATATATAT=0.00 1.0 0.0 0.0 N/A
Other Sub 502 TATATATAT=1.000 TATAT=0.000, TATATAT=0.000, TATATATATAT=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
TopMed Global Study-wide 264690 (TA)4T=0.999996 delATAT=0.000004
14KJPN JAPANESE Study-wide 28250 (TA)4T=0.99993 delAT=0.00007
Allele Frequency Aggregator Total Global 18482 (TA)4T=0.99946 delATAT=0.00000, delAT=0.00054, dupAT=0.00000
Allele Frequency Aggregator European Sub 14120 (TA)4T=0.99929 delATAT=0.00000, delAT=0.00071, dupAT=0.00000
Allele Frequency Aggregator African Sub 2894 (TA)4T=1.0000 delATAT=0.0000, delAT=0.0000, dupAT=0.0000
Allele Frequency Aggregator Latin American 2 Sub 610 (TA)4T=1.000 delATAT=0.000, delAT=0.000, dupAT=0.000
Allele Frequency Aggregator Other Sub 502 (TA)4T=1.000 delATAT=0.000, delAT=0.000, dupAT=0.000
Allele Frequency Aggregator Latin American 1 Sub 146 (TA)4T=1.000 delATAT=0.000, delAT=0.000, dupAT=0.000
Allele Frequency Aggregator Asian Sub 112 (TA)4T=1.000 delATAT=0.000, delAT=0.000, dupAT=0.000
Allele Frequency Aggregator South Asian Sub 98 (TA)4T=1.00 delATAT=0.00, delAT=0.00, dupAT=0.00
8.3KJPN JAPANESE Study-wide 16736 (TA)4T=0.99982 delAT=0.00018
Korean Genome Project KOREAN Study-wide 1820 (TA)4T=0.9995 delAT=0.0005
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 7 NC_000007.14:g.66839116AT[2]
GRCh38.p14 chr 7 NC_000007.14:g.66839116AT[3]
GRCh38.p14 chr 7 NC_000007.14:g.66839116AT[5]
GRCh37.p13 chr 7 NC_000007.13:g.66304103AT[2]
GRCh37.p13 chr 7 NC_000007.13:g.66304103AT[3]
GRCh37.p13 chr 7 NC_000007.13:g.66304103AT[5]
Gene: GTF2IRD1P1, GTF2I repeat domain containing 1 pseudogene 1 (minus strand)
Molecule type Change Amino acid[Codon] SO Term
GTF2IRD1P1 transcript NR_003934.2: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 (TA)4T= delATAT delAT dupAT
GRCh38.p14 chr 7 NC_000007.14:g.66839115_66839123= NC_000007.14:g.66839116AT[2] NC_000007.14:g.66839116AT[3] NC_000007.14:g.66839116AT[5]
GRCh37.p13 chr 7 NC_000007.13:g.66304102_66304110= NC_000007.13:g.66304103AT[2] NC_000007.13:g.66304103AT[3] NC_000007.13:g.66304103AT[5]
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#.

11 SubSNP, 7 Frequency submissions
No Submitter Submission ID Date (Build)
1 SWEGEN ss3001329045 Nov 08, 2017 (151)
2 EVA_DECODE ss3719859536 Jul 13, 2019 (153)
3 KOGIC ss3961724897 Apr 26, 2020 (154)
4 GNOMAD ss4165066324 Apr 26, 2021 (155)
5 GNOMAD ss4165066325 Apr 26, 2021 (155)
6 TOPMED ss4748712915 Apr 26, 2021 (155)
7 TOMMO_GENOMICS ss5183586409 Apr 26, 2021 (155)
8 1000G_HIGH_COVERAGE ss5273224528 Oct 14, 2022 (156)
9 HUGCELL_USP ss5470298044 Oct 14, 2022 (156)
10 TOMMO_GENOMICS ss5723969449 Oct 14, 2022 (156)
11 EVA ss5859215951 Oct 14, 2022 (156)
12 gnomAD - Genomes

Submission ignored due to conflicting rows:
Row 263944205 (NC_000007.14:66839114::TA 3/128070)
Row 263944206 (NC_000007.14:66839114:TA: 88/128070)

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

Submission ignored due to conflicting rows:
Row 263944205 (NC_000007.14:66839114::TA 3/128070)
Row 263944206 (NC_000007.14:66839114:TA: 88/128070)

- Apr 26, 2021 (155)
14 Korean Genome Project NC_000007.14 - 66839115 Apr 26, 2020 (154)
15 8.3KJPN NC_000007.13 - 66304102 Apr 26, 2021 (155)
16 14KJPN NC_000007.14 - 66839115 Oct 14, 2022 (156)
17 TopMed NC_000007.14 - 66839115 Apr 26, 2021 (155)
18 ALFA NC_000007.14 - 66839115 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
586090474, ss4748712915 NC_000007.14:66839114:TATA: NC_000007.14:66839114:TATATATAT:TA…

NC_000007.14:66839114:TATATATAT:TATAT

(self)
3055186862 NC_000007.14:66839114:TATATATAT:TA…

NC_000007.14:66839114:TATATATAT:TATAT

NC_000007.14:66839114:TATATATAT:TA…

NC_000007.14:66839114:TATATATAT:TATAT

(self)
41555716, ss3001329045, ss5183586409 NC_000007.13:66304101:TA: NC_000007.14:66839114:TATATATAT:TA…

NC_000007.14:66839114:TATATATAT:TATATAT

(self)
18102898, 57806553, ss3719859536, ss3961724897, ss4165066325, ss5273224528, ss5470298044, ss5723969449, ss5859215951 NC_000007.14:66839114:TA: NC_000007.14:66839114:TATATATAT:TA…

NC_000007.14:66839114:TATATATAT:TATATAT

(self)
3055186862 NC_000007.14:66839114:TATATATAT:TA…

NC_000007.14:66839114:TATATATAT:TATATAT

NC_000007.14:66839114:TATATATAT:TA…

NC_000007.14:66839114:TATATATAT:TATATAT

(self)
ss4165066324 NC_000007.14:66839114::TA NC_000007.14:66839114:TATATATAT:TA…

NC_000007.14:66839114:TATATATAT:TATATATATAT

(self)
3055186862 NC_000007.14:66839114:TATATATAT:TA…

NC_000007.14:66839114:TATATATAT:TATATATATAT

NC_000007.14:66839114:TATATATAT:TA…

NC_000007.14:66839114:TATATATAT:TATATATATAT

(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 rs1217212087

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