Name: rs1248727219
Published: September 21, 2022
License: Open Access

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.

rs1248727219

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chrX:9188868-9188873 (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: delGC / dupGC
Variation Type: Indel Insertion and Deletion
Frequency: dupGC=0.00086 (80/93068, GnomAD)
dupGC=0.00076 (9/11862, ALFA)
dupGC=0.0015 (7/4805, 1000G_30x) (+ 1 more)
delGC=0.0003 (1/3775, 1000G)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: None
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	GCGCGC=0.99924	GCGCGCGC=0.00076	0.99882	0.000337	0.000843	32
European	Sub	7618	GCGCGC=1.0000	GCGCGCGC=0.0000	1.0	0.0	0.0	N/A
African	Sub	2816	GCGCGC=0.9968	GCGCGCGC=0.0032	0.995028	0.00142	0.003551	32
African Others	Sub	108	GCGCGC=1.000	GCGCGCGC=0.000	1.0	0.0	0.0	N/A
African American	Sub	2708	GCGCGC=0.9967	GCGCGCGC=0.0033	0.99483	0.001477	0.003693	32
Asian	Sub	108	GCGCGC=1.000	GCGCGCGC=0.000	1.0	0.0	0.0	N/A
East Asian	Sub	84	GCGCGC=1.00	GCGCGCGC=0.00	1.0	0.0	0.0	N/A
Other Asian	Sub	24	GCGCGC=1.00	GCGCGCGC=0.00	1.0	0.0	0.0	N/A
Latin American 1	Sub	146	GCGCGC=1.000	GCGCGCGC=0.000	1.0	0.0	0.0	N/A
Latin American 2	Sub	610	GCGCGC=1.000	GCGCGCGC=0.000	1.0	0.0	0.0	N/A
South Asian	Sub	94	GCGCGC=1.00	GCGCGCGC=0.00	1.0	0.0	0.0	N/A
Other	Sub	470	GCGCGC=1.000	GCGCGCGC=0.000	1.0	0.0	0.0	N/A

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").

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Study	Population	Group	Sample Size	Ref Allele	Alt Allele
gnomAD - Genomes	Global	Study-wide	93068	- No frequency provided	dupGC=0.00086
gnomAD - Genomes	European	Sub	56105	- No frequency provided	dupGC=0.00004
gnomAD - Genomes	African	Sub	22100	- No frequency provided	dupGC=0.00344
gnomAD - Genomes	American	Sub	8771	- No frequency provided	dupGC=0.0002
gnomAD - Genomes	Ashkenazi Jewish	Sub	2486	- No frequency provided	dupGC=0.0000
gnomAD - Genomes	East Asian	Sub	2175	- No frequency provided	dupGC=0.0000
gnomAD - Genomes	Other	Sub	1431	- No frequency provided	dupGC=0.0000
Allele Frequency Aggregator	Total	Global	11862	(GC)₃=0.99924	dupGC=0.00076
Allele Frequency Aggregator	European	Sub	7618	(GC)₃=1.0000	dupGC=0.0000
Allele Frequency Aggregator	African	Sub	2816	(GC)₃=0.9968	dupGC=0.0032
Allele Frequency Aggregator	Latin American 2	Sub	610	(GC)₃=1.000	dupGC=0.000
Allele Frequency Aggregator	Other	Sub	470	(GC)₃=1.000	dupGC=0.000
Allele Frequency Aggregator	Latin American 1	Sub	146	(GC)₃=1.000	dupGC=0.000
Allele Frequency Aggregator	Asian	Sub	108	(GC)₃=1.000	dupGC=0.000
Allele Frequency Aggregator	South Asian	Sub	94	(GC)₃=1.00	dupGC=0.00
1000Genomes_30x	Global	Study-wide	4805	- No frequency provided	dupGC=0.0015
1000Genomes_30x	African	Sub	1328	- No frequency provided	dupGC=0.0053
1000Genomes_30x	Europe	Sub	961	- No frequency provided	dupGC=0.000
1000Genomes_30x	South Asian	Sub	883	- No frequency provided	dupGC=0.000
1000Genomes_30x	East Asian	Sub	878	- No frequency provided	dupGC=0.000
1000Genomes_30x	American	Sub	755	- No frequency provided	dupGC=0.000
1000Genomes	Global	Study-wide	3775	(GC)₃=0.9997	delGC=0.0003
1000Genomes	African	Sub	1003	(GC)₃=1.0000	delGC=0.0000
1000Genomes	Europe	Sub	766	(GC)₃=1.000	delGC=0.000
1000Genomes	East Asian	Sub	764	(GC)₃=1.000	delGC=0.000
1000Genomes	South Asian	Sub	718	(GC)₃=0.999	delGC=0.001
1000Genomes	American	Sub	524	(GC)₃=1.000	delGC=0.000

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.9188868GC[2]
GRCh38.p14 chr X	NC_000023.11:g.9188868GC[4]
GRCh37.p13 chr X	NC_000023.10:g.9156909GC[2]
GRCh37.p13 chr X	NC_000023.10:g.9156909GC[4]

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

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	(GC)₃=	delGC	dupGC
GRCh38.p14 chr X	NC_000023.11:g.9188868_9188873=	NC_000023.11:g.9188868GC[2]	NC_000023.11:g.9188868GC[4]
GRCh37.p13 chr X	NC_000023.10:g.9156909_9156914=	NC_000023.10:g.9156909GC[2]	NC_000023.10:g.9156909GC[4]

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, 4 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	1000GENOMES	ss1553482763	Jan 10, 2018 (151)
2	GNOMAD	ss2976418999	Nov 08, 2017 (151)
3	1000G_HIGH_COVERAGE	ss5311779024	Oct 16, 2022 (156)
4	1000G_HIGH_COVERAGE	ss5619596517	Oct 16, 2022 (156)
5	SANFORD_IMAGENETICS	ss5664861887	Oct 16, 2022 (156)
6	1000Genomes	NC_000023.10 - 9156909	Oct 12, 2018 (152)
7	1000Genomes_30x	NC_000023.11 - 9188868	Oct 16, 2022 (156)
8	gnomAD - Genomes	NC_000023.11 - 9188868	Apr 26, 2021 (155)
9	ALFA	NC_000023.11 - 9188868	Apr 26, 2021 (155)

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
81467226, ss1553482763	NC_000023.10:9156908:GC:	NC_000023.11:9188867:GCGCGC:GCGC	(self)
ss2976418999, ss5664861887	NC_000023.10:9156908::GC	NC_000023.11:9188867:GCGCGC:GCGCGC… NC_000023.11:9188867:GCGCGC:GCGCGCGC	(self)
107122452, 575028971, ss5311779024, ss5619596517	NC_000023.11:9188867::GC	NC_000023.11:9188867:GCGCGC:GCGCGC… NC_000023.11:9188867:GCGCGC:GCGCGCGC	(self)
7095410415	NC_000023.11:9188867:GCGCGC:GCGCGC… NC_000023.11:9188867:GCGCGC:GCGCGCGC	NC_000023.11:9188867:GCGCGC:GCGCGC… NC_000023.11:9188867:GCGCGC:GCGCGCGC	(self)

Publications tab displays PubMed articles citing the variation as a listing of PMID, Title, Author, Year, Journal, ordered by Year, descending.

No publications for rs1248727219

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.

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dbSNP Short Genetic Variations

Welcome to the Reference SNP (rs) Report

Reference SNP (rs) Report

rs1248727219