Name: rs1490002666
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.

rs1490002666

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr22:23070611 (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: insGC / insGCTGAGTC
Variation Type: Indel Insertion and Deletion
Frequency: insGC=0.00043 (8/18520, ALFA)
insGC=0.0018 (8/4480, Estonian)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: RSPH14 : Intron Variant
GNAZ : 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	HTRZ	HWEP
Total	Global	18520	C=0.99951	CGC=0.00043, CGCTGAGTC=0.00005	0.999136	0.000864	0
European	Sub	14152	C=0.99936	CGC=0.00057, CGCTGAGTC=0.00007	0.998869	0.001131	0
African	Sub	2898	C=1.0000	CGC=0.0000, CGCTGAGTC=0.0000	1.0	0.0	N/A
African Others	Sub	114	C=1.000	CGC=0.000, CGCTGAGTC=0.000	1.0	0.0	N/A
African American	Sub	2784	C=1.0000	CGC=0.0000, CGCTGAGTC=0.0000	1.0	0.0	N/A
Asian	Sub	112	C=1.000	CGC=0.000, CGCTGAGTC=0.000	1.0	0.0	N/A
East Asian	Sub	86	C=1.00	CGC=0.00, CGCTGAGTC=0.00	1.0	0.0	N/A
Other Asian	Sub	26	C=1.00	CGC=0.00, CGCTGAGTC=0.00	1.0	0.0	N/A
Latin American 1	Sub	146	C=1.000	CGC=0.000, CGCTGAGTC=0.000	1.0	0.0	N/A
Latin American 2	Sub	610	C=1.000	CGC=0.000, CGCTGAGTC=0.000	1.0	0.0	N/A
South Asian	Sub	98	C=1.00	CGC=0.00, CGCTGAGTC=0.00	1.0	0.0	N/A
Other	Sub	504	C=1.000	CGC=0.000, CGCTGAGTC=0.000	1.0	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
Allele Frequency Aggregator	Total	Global	18520	C=0.99951	insGC=0.00043, insGCTGAGTC=0.00005
Allele Frequency Aggregator	European	Sub	14152	C=0.99936	insGC=0.00057, insGCTGAGTC=0.00007
Allele Frequency Aggregator	African	Sub	2898	C=1.0000	insGC=0.0000, insGCTGAGTC=0.0000
Allele Frequency Aggregator	Latin American 2	Sub	610	C=1.000	insGC=0.000, insGCTGAGTC=0.000
Allele Frequency Aggregator	Other	Sub	504	C=1.000	insGC=0.000, insGCTGAGTC=0.000
Allele Frequency Aggregator	Latin American 1	Sub	146	C=1.000	insGC=0.000, insGCTGAGTC=0.000
Allele Frequency Aggregator	Asian	Sub	112	C=1.000	insGC=0.000, insGCTGAGTC=0.000
Allele Frequency Aggregator	South Asian	Sub	98	C=1.00	insGC=0.00, insGCTGAGTC=0.00
Genetic variation in the Estonian population	Estonian	Study-wide	4480	- No frequency provided	insGC=0.0018

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 22	NC_000022.11:g.23070611_23070612insGC
GRCh38.p14 chr 22	NC_000022.11:g.23070611_23070612insGCTGAGTC
GRCh37.p13 chr 22	NC_000022.10:g.23412797_23412798insGC
GRCh37.p13 chr 22	NC_000022.10:g.23412797_23412798insGCTGAGTC

Gene: GNAZ, G protein subunit alpha z (plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
GNAZ transcript	NM_002073.4:c.-450+41_-45… NM_002073.4:c.-450+41_-450+42insGC	N/A	Intron Variant
GNAZ transcript variant X2	XM_017028786.3:c.-450+41_… XM_017028786.3:c.-450+41_-450+42insGC	N/A	Intron Variant
GNAZ transcript variant X1	XM_047441346.1:c.-450+41_… XM_047441346.1:c.-450+41_-450+42insGC	N/A	Intron Variant

Gene: RSPH14, radial spoke head 14 homolog (minus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
RSPH14 transcript	NM_014433.3:c.422-6478_42… NM_014433.3:c.422-6478_422-6477insGC	N/A	Intron Variant
RSPH14 transcript variant X4	XM_011530149.3:c.422-6478… XM_011530149.3:c.422-6478_422-6477insGC	N/A	Intron Variant
RSPH14 transcript variant X1	XM_011530150.2:c.422-6478… XM_011530150.2:c.422-6478_422-6477insGC	N/A	Intron Variant
RSPH14 transcript variant X3	XM_011530151.3:c.422-6478… XM_011530151.3:c.422-6478_422-6477insGC	N/A	Intron Variant
RSPH14 transcript variant X6	XM_011530152.3:c.422-6478… XM_011530152.3:c.422-6478_422-6477insGC	N/A	Intron Variant
RSPH14 transcript variant X5	XM_011530154.3:c.218-6478… XM_011530154.3:c.218-6478_218-6477insGC	N/A	Intron Variant
RSPH14 transcript variant X2	XM_017028774.2:c.422-6478… XM_017028774.2:c.422-6478_422-6477insGC	N/A	Intron Variant
RSPH14 transcript variant X7	XM_011530155.3:c.	N/A	Genic Upstream Transcript Variant
RSPH14 transcript variant X8	XM_047441334.1:c.	N/A	Genic Upstream Transcript Variant

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	C=	insGC	insGCTGAGTC
GRCh38.p14 chr 22	NC_000022.11:g.23070611=	NC_000022.11:g.23070611_23070612insGC	NC_000022.11:g.23070611_23070612insGCTGAGTC
GRCh37.p13 chr 22	NC_000022.10:g.23412797=	NC_000022.10:g.23412797_23412798insGC	NC_000022.10:g.23412797_23412798insGCTGAGTC
GNAZ transcript	NM_002073.2:c.-450+41=	NM_002073.2:c.-450+41_-450+42insGC	NM_002073.2:c.-450+41_-450+42insGCTGAGTC
GNAZ transcript	NM_002073.4:c.-450+41=	NM_002073.4:c.-450+41_-450+42insGC	NM_002073.4:c.-450+41_-450+42insGCTGAGTC
RSPH14 transcript	NM_014433.2:c.422-6486=	NM_014433.2:c.422-6486_422-6485insGC	NM_014433.2:c.422-6486_422-6485insGACTCAGC
RSPH14 transcript	NM_014433.3:c.422-6478=	NM_014433.3:c.422-6478_422-6477insGC	NM_014433.3:c.422-6478_422-6477insGACTCAGC
RTDR1 transcript variant X1	XM_005261568.1:c.554-6486=	XM_005261568.1:c.554-6486_554-6485insGC	XM_005261568.1:c.554-6486_554-6485insGACTCAGC
RSPH14 transcript variant X4	XM_011530149.3:c.422-6478=	XM_011530149.3:c.422-6478_422-6477insGC	XM_011530149.3:c.422-6478_422-6477insGACTCAGC
RSPH14 transcript variant X1	XM_011530150.2:c.422-6478=	XM_011530150.2:c.422-6478_422-6477insGC	XM_011530150.2:c.422-6478_422-6477insGACTCAGC
RSPH14 transcript variant X3	XM_011530151.3:c.422-6478=	XM_011530151.3:c.422-6478_422-6477insGC	XM_011530151.3:c.422-6478_422-6477insGACTCAGC
RSPH14 transcript variant X6	XM_011530152.3:c.422-6478=	XM_011530152.3:c.422-6478_422-6477insGC	XM_011530152.3:c.422-6478_422-6477insGACTCAGC
RSPH14 transcript variant X5	XM_011530154.3:c.218-6478=	XM_011530154.3:c.218-6478_218-6477insGC	XM_011530154.3:c.218-6478_218-6477insGACTCAGC
RSPH14 transcript variant X2	XM_017028774.2:c.422-6478=	XM_017028774.2:c.422-6478_422-6477insGC	XM_017028774.2:c.422-6478_422-6477insGACTCAGC
GNAZ transcript variant X2	XM_017028786.3:c.-450+41=	XM_017028786.3:c.-450+41_-450+42insGC	XM_017028786.3:c.-450+41_-450+42insGCTGAGTC
GNAZ transcript variant X1	XM_047441346.1:c.-450+41=	XM_047441346.1:c.-450+41_-450+42insGC	XM_047441346.1:c.-450+41_-450+42insGCTGAGTC

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#.

3 SubSNP, 4 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	EGCUT_WGS	ss3685649554	Jul 13, 2019 (153)
2	GNOMAD	ss4362942726	Apr 27, 2021 (155)
3	GNOMAD	ss4362942727	Apr 27, 2021 (155)
4	Genetic variation in the Estonian population	NC_000022.10 - 23412797	Oct 12, 2018 (152)
5	gnomAD - Genomes Submission ignored due to conflicting rows: Row 567191539 (NC_000022.11:23070610::CG 14/139894) Row 567191540 (NC_000022.11:23070610::CGCTGAGT 7/139894)	-	Apr 27, 2021 (155)
6	gnomAD - Genomes Submission ignored due to conflicting rows: Row 567191539 (NC_000022.11:23070610::CG 14/139894) Row 567191540 (NC_000022.11:23070610::CGCTGAGT 7/139894)	-	Apr 27, 2021 (155)
7	ALFA	NC_000022.11 - 23070611	Apr 27, 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
31387802, ss3685649554	NC_000022.10:23412796::CG	NC_000022.11:23070610:C:CGC	(self)
ss4362942726	NC_000022.11:23070610::CG	NC_000022.11:23070610:C:CGC	(self)
14348287316	NC_000022.11:23070610:C:CGC	NC_000022.11:23070610:C:CGC	(self)
ss4362942727	NC_000022.11:23070610::CGCTGAGT	NC_000022.11:23070610:C:CGCTGAGTC	(self)
14348287316	NC_000022.11:23070610:C:CGCTGAGTC	NC_000022.11:23070610:C:CGCTGAGTC	(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 rs1490002666

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

rs1490002666