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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.

rs1268475507

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr7:69598310-69598359 (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
delAGCGAAAGC(ACGA)2(GCGA)5GCG / de…

delAGCGAAAGC(ACGA)2(GCGA)5GCG / delAAAGC(ACGA)2(GCGA)5GCG

Variation Type
Indel Insertion and Deletion
Frequency
delAAAGC(ACGA)2(GCGA)5GCG=0.00007 (2/28250, 14KJPN)
delAAAGC(ACGA)2(GCGA)5GCG=0.00012 (2/16752, 8.3KJPN)
delAGCGAAAGC(ACGA)2(GCGA)5GCG=0.00000 (0/11852, ALFA) (+ 1 more)
delAAAGC(ACGA)2(GCGA)5GCG=0.00000 (0/11852, ALFA)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
AUTS2 : 2KB Upstream Variant
CT66 : 2KB Upstream 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 11852 CGAGCGAGCGAGCGAAAGCACGAACGAGCGAGCGAGCGAGCGAGCGAGCG=1.00000 CGAGCGAGCG=0.00000, CGAGCGAGCGAGCG=0.00000 1.0 0.0 0.0 N/A
European Sub 7614 CGAGCGAGCGAGCGAAAGCACGAACGAGCGAGCGAGCGAGCGAGCGAGCG=1.0000 CGAGCGAGCG=0.0000, CGAGCGAGCGAGCG=0.0000 1.0 0.0 0.0 N/A
African Sub 2810 CGAGCGAGCGAGCGAAAGCACGAACGAGCGAGCGAGCGAGCGAGCGAGCG=1.0000 CGAGCGAGCG=0.0000, CGAGCGAGCGAGCG=0.0000 1.0 0.0 0.0 N/A
African Others Sub 108 CGAGCGAGCGAGCGAAAGCACGAACGAGCGAGCGAGCGAGCGAGCGAGCG=1.000 CGAGCGAGCG=0.000, CGAGCGAGCGAGCG=0.000 1.0 0.0 0.0 N/A
African American Sub 2702 CGAGCGAGCGAGCGAAAGCACGAACGAGCGAGCGAGCGAGCGAGCGAGCG=1.0000 CGAGCGAGCG=0.0000, CGAGCGAGCGAGCG=0.0000 1.0 0.0 0.0 N/A
Asian Sub 108 CGAGCGAGCGAGCGAAAGCACGAACGAGCGAGCGAGCGAGCGAGCGAGCG=1.000 CGAGCGAGCG=0.000, CGAGCGAGCGAGCG=0.000 1.0 0.0 0.0 N/A
East Asian Sub 84 CGAGCGAGCGAGCGAAAGCACGAACGAGCGAGCGAGCGAGCGAGCGAGCG=1.00 CGAGCGAGCG=0.00, CGAGCGAGCGAGCG=0.00 1.0 0.0 0.0 N/A
Other Asian Sub 24 CGAGCGAGCGAGCGAAAGCACGAACGAGCGAGCGAGCGAGCGAGCGAGCG=1.00 CGAGCGAGCG=0.00, CGAGCGAGCGAGCG=0.00 1.0 0.0 0.0 N/A
Latin American 1 Sub 146 CGAGCGAGCGAGCGAAAGCACGAACGAGCGAGCGAGCGAGCGAGCGAGCG=1.000 CGAGCGAGCG=0.000, CGAGCGAGCGAGCG=0.000 1.0 0.0 0.0 N/A
Latin American 2 Sub 610 CGAGCGAGCGAGCGAAAGCACGAACGAGCGAGCGAGCGAGCGAGCGAGCG=1.000 CGAGCGAGCG=0.000, CGAGCGAGCGAGCG=0.000 1.0 0.0 0.0 N/A
South Asian Sub 94 CGAGCGAGCGAGCGAAAGCACGAACGAGCGAGCGAGCGAGCGAGCGAGCG=1.00 CGAGCGAGCG=0.00, CGAGCGAGCGAGCG=0.00 1.0 0.0 0.0 N/A
Other Sub 470 CGAGCGAGCGAGCGAAAGCACGAACGAGCGAGCGAGCGAGCGAGCGAGCG=1.000 CGAGCGAGCG=0.000, CGAGCGAGCGAGCG=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 28250 (CGAG)3CGAAAGC(ACGA)2(GCGA)5GCG=0.99993 delAAAGC(ACGA)2(GCGA)5GCG=0.00007
8.3KJPN JAPANESE Study-wide 16752 (CGAG)3CGAAAGC(ACGA)2(GCGA)5GCG=0.99988 delAAAGC(ACGA)2(GCGA)5GCG=0.00012
Allele Frequency Aggregator Total Global 11852 (CGAG)3CGAAAGC(ACGA)2(GCGA)5GCG=1.00000 delAGCGAAAGC(ACGA)2(GCGA)5GCG=0.00000, delAAAGC(ACGA)2(GCGA)5GCG=0.00000
Allele Frequency Aggregator European Sub 7614 (CGAG)3CGAAAGC(ACGA)2(GCGA)5GCG=1.0000 delAGCGAAAGC(ACGA)2(GCGA)5GCG=0.0000, delAAAGC(ACGA)2(GCGA)5GCG=0.0000
Allele Frequency Aggregator African Sub 2810 (CGAG)3CGAAAGC(ACGA)2(GCGA)5GCG=1.0000 delAGCGAAAGC(ACGA)2(GCGA)5GCG=0.0000, delAAAGC(ACGA)2(GCGA)5GCG=0.0000
Allele Frequency Aggregator Latin American 2 Sub 610 (CGAG)3CGAAAGC(ACGA)2(GCGA)5GCG=1.000 delAGCGAAAGC(ACGA)2(GCGA)5GCG=0.000, delAAAGC(ACGA)2(GCGA)5GCG=0.000
Allele Frequency Aggregator Other Sub 470 (CGAG)3CGAAAGC(ACGA)2(GCGA)5GCG=1.000 delAGCGAAAGC(ACGA)2(GCGA)5GCG=0.000, delAAAGC(ACGA)2(GCGA)5GCG=0.000
Allele Frequency Aggregator Latin American 1 Sub 146 (CGAG)3CGAAAGC(ACGA)2(GCGA)5GCG=1.000 delAGCGAAAGC(ACGA)2(GCGA)5GCG=0.000, delAAAGC(ACGA)2(GCGA)5GCG=0.000
Allele Frequency Aggregator Asian Sub 108 (CGAG)3CGAAAGC(ACGA)2(GCGA)5GCG=1.000 delAGCGAAAGC(ACGA)2(GCGA)5GCG=0.000, delAAAGC(ACGA)2(GCGA)5GCG=0.000
Allele Frequency Aggregator South Asian Sub 94 (CGAG)3CGAAAGC(ACGA)2(GCGA)5GCG=1.00 delAGCGAAAGC(ACGA)2(GCGA)5GCG=0.00, delAAAGC(ACGA)2(GCGA)5GCG=0.00
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.69598320_69598359del
GRCh38.p14 chr 7 NC_000007.14:g.69598324_69598359del
GRCh37.p13 chr 7 NC_000007.13:g.69063306_69063345del
GRCh37.p13 chr 7 NC_000007.13:g.69063310_69063345del
AUTS2 RefSeqGene NG_034133.1:g.4402_4441del
AUTS2 RefSeqGene NG_034133.1:g.4406_4441del
Gene: AUTS2, activator of transcription and developmental regulator AUTS2 (plus strand) : 2KB Upstream Variant
Molecule type Change Amino acid[Codon] SO Term
AUTS2 transcript variant 2 NM_001127231.3:c. N/A Upstream Transcript Variant
AUTS2 transcript variant 3 NM_001127232.3:c. N/A Upstream Transcript Variant
AUTS2 transcript variant 1 NM_015570.4:c. N/A Upstream Transcript Variant
AUTS2 transcript variant X1 XM_011516010.3:c. N/A Upstream Transcript Variant
AUTS2 transcript variant X2 XM_011516011.3:c. N/A Upstream Transcript Variant
AUTS2 transcript variant X4 XM_011516012.3:c. N/A Upstream Transcript Variant
AUTS2 transcript variant X6 XM_011516013.3:c. N/A Upstream Transcript Variant
AUTS2 transcript variant X8 XM_011516014.3:c. N/A Upstream Transcript Variant
AUTS2 transcript variant X3 XM_047420154.1:c. N/A Upstream Transcript Variant
AUTS2 transcript variant X5 XM_047420155.1:c. N/A Upstream Transcript Variant
AUTS2 transcript variant X7 XM_047420156.1:c. N/A Upstream Transcript Variant
AUTS2 transcript variant X9 XM_047420157.1:c. N/A Upstream Transcript Variant
AUTS2 transcript variant X10 XM_047420158.1:c. N/A Upstream Transcript Variant
AUTS2 transcript variant X11 XM_047420159.1:c. N/A Upstream Transcript Variant
AUTS2 transcript variant X12 XM_047420160.1:c. N/A Upstream Transcript Variant
AUTS2 transcript variant X13 XM_047420161.1:c. N/A Upstream Transcript Variant
AUTS2 transcript variant X14 XM_047420162.1:c. N/A Upstream Transcript Variant
AUTS2 transcript variant X24 XM_005250257.3:c. N/A N/A
AUTS2 transcript variant X15 XM_011516017.3:c. N/A N/A
AUTS2 transcript variant X23 XM_011516018.3:c. N/A N/A
AUTS2 transcript variant X16 XM_047420163.1:c. N/A N/A
AUTS2 transcript variant X17 XM_047420164.1:c. N/A N/A
AUTS2 transcript variant X18 XM_047420165.1:c. N/A N/A
AUTS2 transcript variant X19 XM_047420166.1:c. N/A N/A
AUTS2 transcript variant X20 XM_047420167.1:c. N/A N/A
AUTS2 transcript variant X21 XM_047420168.1:c. N/A N/A
AUTS2 transcript variant X22 XM_047420169.1:c. N/A N/A
AUTS2 transcript variant X25 XM_047420170.1:c. N/A N/A
AUTS2 transcript variant X26 XM_047420171.1:c. N/A N/A
Gene: CT66, cancer/testis associated transcript 66 (minus strand) : 2KB Upstream Variant
Molecule type Change Amino acid[Codon] SO Term
CT66 transcript variant 1 NR_108105.2:n. N/A Upstream Transcript Variant
CT66 transcript variant 2 NR_148926.1:n. N/A Upstream Transcript Variant
CT66 transcript variant 3 NR_148927.1:n. N/A 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
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 (CGAG)3CGAAAGC(ACGA)2(GCGA)5GCG= delAGCGAAAGC(ACGA)2(GCGA)5GCG delAAAGC(ACGA)2(GCGA)5GCG
GRCh38.p14 chr 7 NC_000007.14:g.69598310_69598359= NC_000007.14:g.69598320_69598359del NC_000007.14:g.69598324_69598359del
GRCh37.p13 chr 7 NC_000007.13:g.69063296_69063345= NC_000007.13:g.69063306_69063345del NC_000007.13:g.69063310_69063345del
AUTS2 RefSeqGene NG_034133.1:g.4392_4441= NG_034133.1:g.4402_4441del NG_034133.1:g.4406_4441del
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#.

8 SubSNP, 5 Frequency submissions
No Submitter Submission ID Date (Build)
1 SWEGEN ss3001368207 Nov 08, 2017 (151)
2 GNOMAD ss4165429460 Apr 26, 2021 (155)
3 GNOMAD ss4165429461 Apr 26, 2021 (155)
4 TOMMO_GENOMICS ss5183692387 Apr 26, 2021 (155)
5 1000G_HIGH_COVERAGE ss5273305124 Oct 14, 2022 (156)
6 HUGCELL_USP ss5470369787 Oct 14, 2022 (156)
7 HUGCELL_USP ss5470369788 Oct 14, 2022 (156)
8 TOMMO_GENOMICS ss5724107832 Oct 14, 2022 (156)
9 gnomAD - Genomes

Submission ignored due to conflicting rows:
Row 264555455 (NC_000007.14:69598309:CGAGCGAGCGAGCGAAAGCACGAACGAGCGAGCGAG: 92/134236)
Row 264555456 (NC_000007.14:69598309:CGAGCGAGCGAGCGAAAGCACGAACGAGCGAGCGAGCGAG: 11/134240)

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

Submission ignored due to conflicting rows:
Row 264555455 (NC_000007.14:69598309:CGAGCGAGCGAGCGAAAGCACGAACGAGCGAGCGAG: 92/134236)
Row 264555456 (NC_000007.14:69598309:CGAGCGAGCGAGCGAAAGCACGAACGAGCGAGCGAGCGAG: 11/134240)

- Apr 26, 2021 (155)
11 8.3KJPN NC_000007.13 - 69063296 Apr 26, 2021 (155)
12 14KJPN NC_000007.14 - 69598310 Oct 14, 2022 (156)
13 ALFA NC_000007.14 - 69598310 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
ss4165429461, ss5470369787 NC_000007.14:69598309:CGAGCGAGCGAG…

NC_000007.14:69598309:CGAGCGAGCGAGCGAAAGCACGAACGAGCGAGCGAGCGAG:

NC_000007.14:69598309:CGAGCGAGCGAG…

NC_000007.14:69598309:CGAGCGAGCGAGCGAAAGCACGAACGAGCGAGCGAGCGAGCGAGCGAGCG:CGAGCGAGCG

(self)
3283868301 NC_000007.14:69598309:CGAGCGAGCGAG…

NC_000007.14:69598309:CGAGCGAGCGAGCGAAAGCACGAACGAGCGAGCGAGCGAGCGAGCGAGCG:CGAGCGAGCG

NC_000007.14:69598309:CGAGCGAGCGAG…

NC_000007.14:69598309:CGAGCGAGCGAGCGAAAGCACGAACGAGCGAGCGAGCGAGCGAGCGAGCG:CGAGCGAGCG

(self)
41661694, ss3001368207, ss5183692387 NC_000007.13:69063295:CGAGCGAGCGAG…

NC_000007.13:69063295:CGAGCGAGCGAGCGAAAGCACGAACGAGCGAGCGAG:

NC_000007.14:69598309:CGAGCGAGCGAG…

NC_000007.14:69598309:CGAGCGAGCGAGCGAAAGCACGAACGAGCGAGCGAGCGAGCGAGCGAGCG:CGAGCGAGCGAGCG

(self)
57944936, ss4165429460, ss5273305124, ss5470369788, ss5724107832 NC_000007.14:69598309:CGAGCGAGCGAG…

NC_000007.14:69598309:CGAGCGAGCGAGCGAAAGCACGAACGAGCGAGCGAG:

NC_000007.14:69598309:CGAGCGAGCGAG…

NC_000007.14:69598309:CGAGCGAGCGAGCGAAAGCACGAACGAGCGAGCGAGCGAGCGAGCGAGCG:CGAGCGAGCGAGCG

(self)
3283868301 NC_000007.14:69598309:CGAGCGAGCGAG…

NC_000007.14:69598309:CGAGCGAGCGAGCGAAAGCACGAACGAGCGAGCGAGCGAGCGAGCGAGCG:CGAGCGAGCGAGCG

NC_000007.14:69598309:CGAGCGAGCGAG…

NC_000007.14:69598309:CGAGCGAGCGAGCGAAAGCACGAACGAGCGAGCGAGCGAGCGAGCGAGCG:CGAGCGAGCGAGCG

(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 rs1268475507

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