Name: rs1491575121
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.

rs1491575121

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr7:6774754-6774756 (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: delGT
Variation Type: Indel Insertion and Deletion
Frequency: delGT=0.00056 (47/84462, GnomAD)
delGT=0.00049 (12/24456, 14KJPN)
delGT=0.00073 (11/15072, 8.3KJPN) (+ 1 more)
delGT=0.00034 (4/11862, ALFA)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: RSPH10B2 : 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	11862	TGT=0.99966	T=0.00034	0.999326	0.000674	0
European	Sub	7618	TGT=0.9996	T=0.0004	0.999212	0.000788	0
African	Sub	2816	TGT=1.0000	T=0.0000	1.0	0.0	N/A
African Others	Sub	108	TGT=1.000	T=0.000	1.0	0.0	N/A
African American	Sub	2708	TGT=1.0000	T=0.0000	1.0	0.0	N/A
Asian	Sub	108	TGT=0.991	T=0.009	0.981481	0.018519	0
East Asian	Sub	84	TGT=1.00	T=0.00	1.0	0.0	N/A
Other Asian	Sub	24	TGT=0.96	T=0.04	0.916667	0.083333	0
Latin American 1	Sub	146	TGT=1.000	T=0.000	1.0	0.0	N/A
Latin American 2	Sub	610	TGT=1.000	T=0.000	1.0	0.0	N/A
South Asian	Sub	94	TGT=1.00	T=0.00	1.0	0.0	N/A
Other	Sub	470	TGT=1.000	T=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
gnomAD - Genomes	Global	Study-wide	84462	TGT=0.99944	delGT=0.00056
gnomAD - Genomes	European	Sub	49726	TGT=0.99954	delGT=0.00046
gnomAD - Genomes	African	Sub	23516	TGT=0.99962	delGT=0.00038
gnomAD - Genomes	American	Sub	6398	TGT=0.9992	delGT=0.0008
gnomAD - Genomes	Ashkenazi Jewish	Sub	2260	TGT=0.9978	delGT=0.0022
gnomAD - Genomes	East Asian	Sub	1352	TGT=0.9970	delGT=0.0030
gnomAD - Genomes	Other	Sub	1210	TGT=0.9992	delGT=0.0008
14KJPN	JAPANESE	Study-wide	24456	TGT=0.99951	delGT=0.00049
8.3KJPN	JAPANESE	Study-wide	15072	TGT=0.99927	delGT=0.00073
Allele Frequency Aggregator	Total	Global	11862	TGT=0.99966	delGT=0.00034
Allele Frequency Aggregator	European	Sub	7618	TGT=0.9996	delGT=0.0004
Allele Frequency Aggregator	African	Sub	2816	TGT=1.0000	delGT=0.0000
Allele Frequency Aggregator	Latin American 2	Sub	610	TGT=1.000	delGT=0.000
Allele Frequency Aggregator	Other	Sub	470	TGT=1.000	delGT=0.000
Allele Frequency Aggregator	Latin American 1	Sub	146	TGT=1.000	delGT=0.000
Allele Frequency Aggregator	Asian	Sub	108	TGT=0.991	delGT=0.009
Allele Frequency Aggregator	South Asian	Sub	94	TGT=1.00	delGT=0.00

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.6774755_6774756del
GRCh37.p13 chr 7	NC_000007.13:g.6814386_6814387del

Gene: RSPH10B2, radial spoke head 10 homolog B2 (plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
RSPH10B2 transcript	NM_001099697.2:c.1224+128… NM_001099697.2:c.1224+1284_1224+1285del	N/A	Intron Variant
RSPH10B2 transcript variant X11	XM_005249833.5:c.600+1284… XM_005249833.5:c.600+1284_600+1285del	N/A	Intron Variant
RSPH10B2 transcript variant X3	XM_006715766.3:c.1239+128… XM_006715766.3:c.1239+1284_1239+1285del	N/A	Intron Variant
RSPH10B2 transcript variant X4	XM_011515491.2:c.1239+128… XM_011515491.2:c.1239+1284_1239+1285del	N/A	Intron Variant
RSPH10B2 transcript variant X5	XM_011515493.2:c.1239+128… XM_011515493.2:c.1239+1284_1239+1285del	N/A	Intron Variant
RSPH10B2 transcript variant X2	XM_024446902.2:c.1239+128… XM_024446902.2:c.1239+1284_1239+1285del	N/A	Intron Variant
RSPH10B2 transcript variant X6	XM_024446903.2:c.1224+128… XM_024446903.2:c.1224+1284_1224+1285del	N/A	Intron Variant
RSPH10B2 transcript variant X7	XM_024446904.2:c.1239+128… XM_024446904.2:c.1239+1284_1239+1285del	N/A	Intron Variant
RSPH10B2 transcript variant X8	XM_024446905.2:c.1224+128… XM_024446905.2:c.1224+1284_1224+1285del	N/A	Intron Variant
RSPH10B2 transcript variant X10	XM_024446906.2:c.1239+128… XM_024446906.2:c.1239+1284_1239+1285del	N/A	Intron Variant
RSPH10B2 transcript variant X13	XM_024446908.2:c.1239+128… XM_024446908.2:c.1239+1284_1239+1285del	N/A	Intron Variant
RSPH10B2 transcript variant X1	XM_047420782.1:c.1239+128… XM_047420782.1:c.1239+1284_1239+1285del	N/A	Intron Variant
RSPH10B2 transcript variant X9	XM_047420783.1:c.1224+128… XM_047420783.1:c.1224+1284_1224+1285del	N/A	Intron Variant
RSPH10B2 transcript variant X12	XM_047420784.1:c.585+1284… XM_047420784.1:c.585+1284_585+1285del	N/A	Intron 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	TGT=	delGT
GRCh38.p14 chr 7	NC_000007.14:g.6774754_6774756=	NC_000007.14:g.6774755_6774756del
GRCh37.p13 chr 7	NC_000007.13:g.6814385_6814387=	NC_000007.13:g.6814386_6814387del
RSPH10B2 transcript	NM_001099697.1:c.1224+1283=	NM_001099697.1:c.1224+1284_1224+1285del
RSPH10B2 transcript	NM_001099697.2:c.1224+1283=	NM_001099697.2:c.1224+1284_1224+1285del
RSPH10B2 transcript variant X1	XM_005249830.1:c.1224+1283=	XM_005249830.1:c.1224+1284_1224+1285del
RSPH10B2 transcript variant X2	XM_005249831.1:c.1239+1283=	XM_005249831.1:c.1239+1284_1239+1285del
RSPH10B2 transcript variant X3	XM_005249832.1:c.1239+1283=	XM_005249832.1:c.1239+1284_1239+1285del
RSPH10B2 transcript variant X4	XM_005249833.1:c.600+1283=	XM_005249833.1:c.600+1284_600+1285del
RSPH10B2 transcript variant X11	XM_005249833.5:c.600+1283=	XM_005249833.5:c.600+1284_600+1285del
RSPH10B2 transcript variant X5	XM_005249834.1:c.1239+1283=	XM_005249834.1:c.1239+1284_1239+1285del
RSPH10B2 transcript variant X3	XM_006715766.3:c.1239+1283=	XM_006715766.3:c.1239+1284_1239+1285del
RSPH10B2 transcript variant X4	XM_011515491.2:c.1239+1283=	XM_011515491.2:c.1239+1284_1239+1285del
RSPH10B2 transcript variant X5	XM_011515493.2:c.1239+1283=	XM_011515493.2:c.1239+1284_1239+1285del
RSPH10B2 transcript variant X2	XM_024446902.2:c.1239+1283=	XM_024446902.2:c.1239+1284_1239+1285del
RSPH10B2 transcript variant X6	XM_024446903.2:c.1224+1283=	XM_024446903.2:c.1224+1284_1224+1285del
RSPH10B2 transcript variant X7	XM_024446904.2:c.1239+1283=	XM_024446904.2:c.1239+1284_1239+1285del
RSPH10B2 transcript variant X8	XM_024446905.2:c.1224+1283=	XM_024446905.2:c.1224+1284_1224+1285del
RSPH10B2 transcript variant X10	XM_024446906.2:c.1239+1283=	XM_024446906.2:c.1239+1284_1239+1285del
RSPH10B2 transcript variant X13	XM_024446908.2:c.1239+1283=	XM_024446908.2:c.1239+1284_1239+1285del
RSPH10B2 transcript variant X1	XM_047420782.1:c.1239+1283=	XM_047420782.1:c.1239+1284_1239+1285del
RSPH10B2 transcript variant X9	XM_047420783.1:c.1224+1283=	XM_047420783.1:c.1224+1284_1224+1285del
RSPH10B2 transcript variant X12	XM_047420784.1:c.585+1283=	XM_047420784.1:c.585+1284_585+1285del

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#.

4 SubSNP, 4 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	GNOMAD	ss2849242936	Jan 10, 2018 (151)
2	TOMMO_GENOMICS	ss5181612663	Apr 26, 2021 (155)
3	TOMMO_GENOMICS	ss5721012181	Oct 13, 2022 (156)
4	YY_MCH	ss5808290467	Oct 13, 2022 (156)
5	gnomAD - Genomes	NC_000007.14 - 6774754	Apr 26, 2021 (155)
6	8.3KJPN	NC_000007.13 - 6814385	Apr 26, 2021 (155)
7	14KJPN	NC_000007.14 - 6774754	Oct 13, 2022 (156)
8	ALFA	NC_000007.14 - 6774754	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
39581970, ss2849242936, ss5181612663	NC_000007.13:6814384:TG:	NC_000007.14:6774753:TGT:T	(self)
251571556, 54849285, ss5721012181, ss5808290467	NC_000007.14:6774753:TG:	NC_000007.14:6774753:TGT:T	(self)
7142076149	NC_000007.14:6774753:TGT:T	NC_000007.14:6774753:TGT:T	(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 rs1491575121

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.

Choose placement

dbSNP Short Genetic Variations

Welcome to the Reference SNP (rs) Report

Reference SNP (rs) Report

rs1491575121