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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.

rs1459563028

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chrX:141503085-141503087 (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
insACCGG / insACGGCCTT(CGG)2 / ins…

insACCGG / insACGGCCTT(CGG)2 / insAGGGTGTTGAGCGG

Variation Type
Indel Insertion and Deletion
Frequency
insAGGGTGTTGAGCGG=0.00008 (3/36300, GnomAD)
insAGGGTGTTGAGCGG=0.00016 (3/19012, 14KJPN)
insAGGGTGTTGAGCGG=0.00000 (0/11862, ALFA)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
SPANXA2-OT1 : 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: 20231103111315
Population Group Sample Size Ref Allele Alt Allele Ref HMOZ Alt HMOZ HTRZ HWEP
Total Global 11862 CGG=1.00000 CGGAGGGTGTTGAGCGG=0.00000 1.0 0.0 0.0 N/A
European Sub 7618 CGG=1.0000 CGGAGGGTGTTGAGCGG=0.0000 1.0 0.0 0.0 N/A
African Sub 2816 CGG=1.0000 CGGAGGGTGTTGAGCGG=0.0000 1.0 0.0 0.0 N/A
African Others Sub 108 CGG=1.000 CGGAGGGTGTTGAGCGG=0.000 1.0 0.0 0.0 N/A
African American Sub 2708 CGG=1.0000 CGGAGGGTGTTGAGCGG=0.0000 1.0 0.0 0.0 N/A
Asian Sub 108 CGG=1.000 CGGAGGGTGTTGAGCGG=0.000 1.0 0.0 0.0 N/A
East Asian Sub 84 CGG=1.00 CGGAGGGTGTTGAGCGG=0.00 1.0 0.0 0.0 N/A
Other Asian Sub 24 CGG=1.00 CGGAGGGTGTTGAGCGG=0.00 1.0 0.0 0.0 N/A
Latin American 1 Sub 146 CGG=1.000 CGGAGGGTGTTGAGCGG=0.000 1.0 0.0 0.0 N/A
Latin American 2 Sub 610 CGG=1.000 CGGAGGGTGTTGAGCGG=0.000 1.0 0.0 0.0 N/A
South Asian Sub 94 CGG=1.00 CGGAGGGTGTTGAGCGG=0.00 1.0 0.0 0.0 N/A
Other Sub 470 CGG=1.000 CGGAGGGTGTTGAGCGG=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
gnomAD - Genomes Global Study-wide 36300 -

No frequency provided

insAGGGTGTTGAGCGG=0.00008
gnomAD - Genomes European Sub 15812 -

No frequency provided

insAGGGTGTTGAGCGG=0.00000
gnomAD - Genomes African Sub 14908 -

No frequency provided

insAGGGTGTTGAGCGG=0.00020
gnomAD - Genomes American Sub 2755 -

No frequency provided

insAGGGTGTTGAGCGG=0.0000
gnomAD - Genomes East Asian Sub 1602 -

No frequency provided

insAGGGTGTTGAGCGG=0.0000
gnomAD - Genomes Ashkenazi Jewish Sub 648 -

No frequency provided

insAGGGTGTTGAGCGG=0.000
gnomAD - Genomes Other Sub 575 -

No frequency provided

insAGGGTGTTGAGCGG=0.000
14KJPN JAPANESE Study-wide 19012 -

No frequency provided

insAGGGTGTTGAGCGG=0.00016
Allele Frequency Aggregator Total Global 11862 CGG=1.00000 insAGGGTGTTGAGCGG=0.00000
Allele Frequency Aggregator European Sub 7618 CGG=1.0000 insAGGGTGTTGAGCGG=0.0000
Allele Frequency Aggregator African Sub 2816 CGG=1.0000 insAGGGTGTTGAGCGG=0.0000
Allele Frequency Aggregator Latin American 2 Sub 610 CGG=1.000 insAGGGTGTTGAGCGG=0.000
Allele Frequency Aggregator Other Sub 470 CGG=1.000 insAGGGTGTTGAGCGG=0.000
Allele Frequency Aggregator Latin American 1 Sub 146 CGG=1.000 insAGGGTGTTGAGCGG=0.000
Allele Frequency Aggregator Asian Sub 108 CGG=1.000 insAGGGTGTTGAGCGG=0.000
Allele Frequency Aggregator South Asian Sub 94 CGG=1.00 insAGGGTGTTGAGCGG=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 X NC_000023.11:g.141503087_141503088insACCGG
GRCh38.p14 chr X NC_000023.11:g.141503087_141503088insACGGCCTTCGGCGG
GRCh38.p14 chr X NC_000023.11:g.141503087_141503088insAGGGTGTTGAGCGG
GRCh37.p13 chr X fix patch HG1453_PATCH NW_004070888.1:g.598890_598891insACCGG
GRCh37.p13 chr X fix patch HG1453_PATCH NW_004070888.1:g.598890_598891insACGGCCTTCGGCGG
GRCh37.p13 chr X fix patch HG1453_PATCH NW_004070888.1:g.598890_598891insAGGGTGTTGAGCGG
GRCh37.p13 chr X NC_000023.10:g.140591095_140591096insACCGG
GRCh37.p13 chr X NC_000023.10:g.140591082_140591095dup
GRCh37.p13 chr X NC_000023.10:g.140591095_140591096insAGGGTGTTGAGCGG
Gene: SPANXA2-OT1, SPANXA2 overlapping transcript 1 (plus strand)
Molecule type Change Amino acid[Codon] SO Term
SPANXA2-OT1 transcript NR_037183.2:n.239_240insA…

NR_037183.2:n.239_240insACCGG

N/A Non Coding Transcript Variant
SPANXA2-OT1 transcript NR_037183.2:n.239_240insA…

NR_037183.2:n.239_240insACGGCCTTCGGCGG

N/A Non Coding Transcript Variant
SPANXA2-OT1 transcript NR_037183.2:n.239_240insA…

NR_037183.2:n.239_240insAGGGTGTTGAGCGG

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 CGG= insACCGG insACGGCCTT(CGG)2 insAGGGTGTTGAGCGG
GRCh38.p14 chr X NC_000023.11:g.141503085_141503087= NC_000023.11:g.141503087_141503088insACCGG NC_000023.11:g.141503087_141503088insACGGCCTTCGGCGG NC_000023.11:g.141503087_141503088insAGGGTGTTGAGCGG
GRCh37.p13 chr X fix patch HG1453_PATCH NW_004070888.1:g.598888_598890= NW_004070888.1:g.598890_598891insACCGG NW_004070888.1:g.598890_598891insACGGCCTTCGGCGG NW_004070888.1:g.598890_598891insAGGGTGTTGAGCGG
GRCh37.p13 chr X NC_000023.10:g.140591079_140591095= NC_000023.10:g.140591095_140591096insACCGG NC_000023.10:g.140591082_140591095dup NC_000023.10:g.140591095_140591096insAGGGTGTTGAGCGG
SPANXA2-OT1 transcript NR_037183.2:n.237_239= NR_037183.2:n.239_240insACCGG NR_037183.2:n.239_240insACGGCCTTCGGCGG NR_037183.2:n.239_240insAGGGTGTTGAGCGG
SPANXA2-OT1 transcript NR_037183.1:n.237_253= NR_037183.1:n.237_241dup NR_037183.1:n.240_253dup NR_037183.1:n.240_241insGGGTGTTGAGCGGA
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#.

5 SubSNP, 3 Frequency submissions
No Submitter Submission ID Date (Build)
1 GNOMAD ss2984005407 Oct 12, 2018 (152)
2 MCHAISSO ss3064382986 Nov 08, 2017 (151)
3 GNOMAD ss4379622743 Apr 26, 2021 (155)
4 TOMMO_GENOMICS ss5236515680 Apr 26, 2021 (155)
5 TOMMO_GENOMICS ss5798963627 Oct 13, 2022 (156)
6 gnomAD - Genomes NC_000023.11 - 141503085 Apr 26, 2021 (155)
7 14KJPN NC_000023.11 - 141503085 Oct 13, 2022 (156)
8 ALFA NC_000023.11 - 141503085 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
94484987, ss5236515680 NC_000023.10:140591059:GGTGTTGAGCG…

NC_000023.10:140591059:GGTGTTGAGCGGTGGTGGACGGAC:GGTGTTGAGCGGTGGTGGACGGAC

NC_000023.11:141503084:CGG:CGGACCGG (self)
ss3064382986 NC_000023.11:141503084::CGGACGGCCT…

NC_000023.11:141503084::CGGACGGCCTTCGG

NC_000023.11:141503084:CGG:CGGACGG…

NC_000023.11:141503084:CGG:CGGACGGCCTTCGGCGG

(self)
592821933, 132800731, ss4379622743, ss5798963627 NC_000023.11:141503084::CGGAGGGTGT…

NC_000023.11:141503084::CGGAGGGTGTTGAG

NC_000023.11:141503084:CGG:CGGAGGG…

NC_000023.11:141503084:CGG:CGGAGGGTGTTGAGCGG

(self)
899036015 NC_000023.11:141503084:CGG:CGGAGGG…

NC_000023.11:141503084:CGG:CGGAGGGTGTTGAGCGG

NC_000023.11:141503084:CGG:CGGAGGG…

NC_000023.11:141503084:CGG:CGGAGGGTGTTGAGCGG

(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 rs1459563028

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