Name: rs78616268
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.

rs78616268

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr15:68933347-68933359 (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: delCA / dupCA / dupCACA
Variation Type: Indel Insertion and Deletion
Frequency: dupCA=0.068212 (18055/264690, TOPMED)
dupCA=0.19648 (5552/28258, 14KJPN)
dupCA=0.02425 (418/17238, ALFA) (+ 8 more)
dupCA=0.19379 (3248/16760, 8.3KJPN)
dupCA=0.1020 (511/5008, 1000G)
dupCA=0.0478 (214/4480, Estonian)
dupCA=0.1681 (308/1832, Korea1K)
dupCA=0.080 (80/998, GoNL)
dupCA=0.065 (39/600, NorthernSweden)
dupCA=0.193 (41/212, Vietnamese)
dupCA=0.12 (5/40, GENOME_DK)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: NOX5 : Intron Variant
SPESP1 : 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	Alt HMOZ	HTRZ	HWEP
Total	Global	17238	ACACACACACACA=0.97575	ACACACACACA=0.00000, ACACACACACACACA=0.02425, ACACACACACACACACA=0.00000	0.952663	0.00116	0.046177	3
European	Sub	13468	ACACACACACACA=0.97446	ACACACACACA=0.00000, ACACACACACACACA=0.02554, ACACACACACACACACA=0.00000	0.950104	0.001188	0.048708	2
African	Sub	2482	ACACACACACACA=0.9714	ACACACACACA=0.0000, ACACACACACACACA=0.0286, ACACACACACACACACA=0.0000	0.9444	0.001612	0.053989	1
African Others	Sub	96	ACACACACACACA=0.93	ACACACACACA=0.00, ACACACACACACACA=0.07, ACACACACACACACACA=0.00	0.854167	0.0	0.145833	0
African American	Sub	2386	ACACACACACACA=0.9732	ACACACACACA=0.0000, ACACACACACACACA=0.0268, ACACACACACACACACA=0.0000	0.94803	0.001676	0.050293	1
Asian	Sub	72	ACACACACACACA=0.99	ACACACACACA=0.00, ACACACACACACACA=0.01, ACACACACACACACACA=0.00	0.972222	0.0	0.027778	0
East Asian	Sub	52	ACACACACACACA=1.00	ACACACACACA=0.00, ACACACACACACACA=0.00, ACACACACACACACACA=0.00	1.0	0.0	0.0	N/A
Other Asian	Sub	20	ACACACACACACA=0.95	ACACACACACA=0.00, ACACACACACACACA=0.05, ACACACACACACACACA=0.00	0.9	0.0	0.1	0
Latin American 1	Sub	132	ACACACACACACA=1.000	ACACACACACA=0.000, ACACACACACACACA=0.000, ACACACACACACACACA=0.000	1.0	0.0	0.0	N/A
Latin American 2	Sub	544	ACACACACACACA=1.000	ACACACACACA=0.000, ACACACACACACACA=0.000, ACACACACACACACACA=0.000	1.0	0.0	0.0	N/A
South Asian	Sub	86	ACACACACACACA=1.00	ACACACACACA=0.00, ACACACACACACACA=0.00, ACACACACACACACACA=0.00	1.0	0.0	0.0	N/A
Other	Sub	454	ACACACACACACA=0.996	ACACACACACA=0.000, ACACACACACACACA=0.004, ACACACACACACACACA=0.000	0.991189	0.0	0.008811	0

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
TopMed	Global	Study-wide	264690	- No frequency provided	dupCA=0.068212
14KJPN	JAPANESE	Study-wide	28258	- No frequency provided	dupCA=0.19648
Allele Frequency Aggregator	Total	Global	17238	(AC)₆A=0.97575	delCA=0.00000, dupCA=0.02425, dupCACA=0.00000
Allele Frequency Aggregator	European	Sub	13468	(AC)₆A=0.97446	delCA=0.00000, dupCA=0.02554, dupCACA=0.00000
Allele Frequency Aggregator	African	Sub	2482	(AC)₆A=0.9714	delCA=0.0000, dupCA=0.0286, dupCACA=0.0000
Allele Frequency Aggregator	Latin American 2	Sub	544	(AC)₆A=1.000	delCA=0.000, dupCA=0.000, dupCACA=0.000
Allele Frequency Aggregator	Other	Sub	454	(AC)₆A=0.996	delCA=0.000, dupCA=0.004, dupCACA=0.000
Allele Frequency Aggregator	Latin American 1	Sub	132	(AC)₆A=1.000	delCA=0.000, dupCA=0.000, dupCACA=0.000
Allele Frequency Aggregator	South Asian	Sub	86	(AC)₆A=1.00	delCA=0.00, dupCA=0.00, dupCACA=0.00
Allele Frequency Aggregator	Asian	Sub	72	(AC)₆A=0.99	delCA=0.00, dupCA=0.01, dupCACA=0.00
8.3KJPN	JAPANESE	Study-wide	16760	- No frequency provided	dupCA=0.19379
1000Genomes	Global	Study-wide	5008	- No frequency provided	dupCA=0.1020
1000Genomes	African	Sub	1322	- No frequency provided	dupCA=0.1120
1000Genomes	East Asian	Sub	1008	- No frequency provided	dupCA=0.1895
1000Genomes	Europe	Sub	1006	- No frequency provided	dupCA=0.0507
1000Genomes	South Asian	Sub	978	- No frequency provided	dupCA=0.096
1000Genomes	American	Sub	694	- No frequency provided	dupCA=0.039
Genetic variation in the Estonian population	Estonian	Study-wide	4480	- No frequency provided	dupCA=0.0478
Korean Genome Project	KOREAN	Study-wide	1832	- No frequency provided	dupCA=0.1681
Genome of the Netherlands Release 5	Genome of the Netherlands	Study-wide	998	- No frequency provided	dupCA=0.080
Northern Sweden	ACPOP	Study-wide	600	- No frequency provided	dupCA=0.065
A Vietnamese Genetic Variation Database	Global	Study-wide	212	- No frequency provided	dupCA=0.193
The Danish reference pan genome	Danish	Study-wide	40	- No frequency provided	dupCA=0.12

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 15	NC_000015.10:g.68933348CA[5]
GRCh38.p14 chr 15	NC_000015.10:g.68933348CA[7]
GRCh38.p14 chr 15	NC_000015.10:g.68933348CA[8]
GRCh37.p13 chr 15	NC_000015.9:g.69225687CA[5]
GRCh37.p13 chr 15	NC_000015.9:g.69225687CA[7]
GRCh37.p13 chr 15	NC_000015.9:g.69225687CA[8]
NOX5 RefSeqGene	NG_030464.1:g.7849CA[5]
NOX5 RefSeqGene	NG_030464.1:g.7849CA[7]
NOX5 RefSeqGene	NG_030464.1:g.7849CA[8]

Gene: NOX5, NADPH oxidase 5 (plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
SPESP1-NOX5 transcript variant 1	NM_001184780.2:c.29+2630A… NM_001184780.2:c.29+2630AC[5]	N/A	Intron Variant
NOX5 transcript variant 2	NM_001184779.2:c.	N/A	Genic Upstream Transcript Variant
NOX5 transcript variant 1	NM_024505.4:c.	N/A	Genic Upstream Transcript Variant
SPESP1-NOX5 transcript variant 2	NR_033671.3:n.	N/A	Intron Variant
SPESP1-NOX5 transcript variant 3	NR_033672.2:n.	N/A	Intron Variant

Gene: SPESP1, sperm equatorial segment protein 1 (plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
SPESP1 transcript	NM_145658.4:c.64+2630AC[5]	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	(AC)₆A=	delCA	dupCA	dupCACA
GRCh38.p14 chr 15	NC_000015.10:g.68933347_68933359=	NC_000015.10:g.68933348CA[5]	NC_000015.10:g.68933348CA[7]	NC_000015.10:g.68933348CA[8]
GRCh37.p13 chr 15	NC_000015.9:g.69225686_69225698=	NC_000015.9:g.69225687CA[5]	NC_000015.9:g.69225687CA[7]	NC_000015.9:g.69225687CA[8]
NOX5 RefSeqGene	NG_030464.1:g.7848_7860=	NG_030464.1:g.7849CA[5]	NG_030464.1:g.7849CA[7]	NG_030464.1:g.7849CA[8]
NOX5 transcript variant 3	NM_001184780.1:c.29+2630=	NM_001184780.1:c.29+2630AC[5]	NM_001184780.1:c.29+2630AC[7]	NM_001184780.1:c.29+2630AC[8]
SPESP1-NOX5 transcript variant 1	NM_001184780.2:c.29+2630=	NM_001184780.2:c.29+2630AC[5]	NM_001184780.2:c.29+2630AC[7]	NM_001184780.2:c.29+2630AC[8]
SPESP1 transcript	NM_145658.3:c.64+2630=	NM_145658.3:c.64+2630AC[5]	NM_145658.3:c.64+2630AC[7]	NM_145658.3:c.64+2630AC[8]
SPESP1 transcript	NM_145658.4:c.64+2630=	NM_145658.4:c.64+2630AC[5]	NM_145658.4:c.64+2630AC[7]	NM_145658.4:c.64+2630AC[8]

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#.

43 SubSNP, 17 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	BCMHGSC_JDW	ss103834044	Dec 06, 2013 (138)
2	GMI	ss289264916	May 04, 2012 (137)
3	GMI	ss289264917	May 04, 2012 (137)
4	1000GENOMES	ss327681449	May 09, 2011 (134)
5	1000GENOMES	ss327798453	May 09, 2011 (134)
6	1000GENOMES	ss328169826	May 09, 2011 (134)
7	LUNTER	ss552428518	Apr 25, 2013 (138)
8	LUNTER	ss552752833	Apr 25, 2013 (138)
9	LUNTER	ss553578150	Apr 25, 2013 (138)
10	TISHKOFF	ss564017449	Apr 25, 2013 (138)
11	SSMP	ss664283834	Apr 01, 2015 (144)
12	EVA-GONL	ss991916535	Aug 21, 2014 (142)
13	1000GENOMES	ss1375048854	Aug 21, 2014 (142)
14	EVA_GENOME_DK	ss1574877635	Apr 01, 2015 (144)
15	EVA_UK10K_ALSPAC	ss1708343588	Jan 10, 2018 (151)
16	EVA_UK10K_TWINSUK	ss1708343593	Jan 10, 2018 (151)
17	EVA_UK10K_TWINSUK	ss1710673517	Apr 01, 2015 (144)
18	EVA_UK10K_ALSPAC	ss1710673518	Apr 01, 2015 (144)
19	GENOMED	ss1968139335	Jul 19, 2016 (147)
20	JJLAB	ss2031273102	Sep 14, 2016 (149)
21	SYSTEMSBIOZJU	ss2628716395	Nov 08, 2017 (151)
22	SWEGEN	ss3013487745	Nov 08, 2017 (151)
23	EGCUT_WGS	ss3680634634	Jul 13, 2019 (153)
24	EVA_DECODE	ss3698144343	Jul 13, 2019 (153)
25	EVA_DECODE	ss3698144344	Jul 13, 2019 (153)
26	ACPOP	ss3741033889	Jul 13, 2019 (153)
27	KHV_HUMAN_GENOMES	ss3818556073	Jul 13, 2019 (153)
28	EVA	ss3840749744	Apr 27, 2020 (154)
29	EVA	ss3846239235	Apr 27, 2020 (154)
30	KOGIC	ss3976396222	Apr 27, 2020 (154)
31	GNOMAD	ss4290990999	Apr 26, 2021 (155)
32	GNOMAD	ss4290991000	Apr 26, 2021 (155)
33	TOPMED	ss4995837383	Apr 26, 2021 (155)
34	TOMMO_GENOMICS	ss5216782987	Apr 26, 2021 (155)
35	1000G_HIGH_COVERAGE	ss5298885979	Oct 16, 2022 (156)
36	HUGCELL_USP	ss5492572052	Oct 16, 2022 (156)
37	EVA	ss5511472960	Oct 16, 2022 (156)
38	SANFORD_IMAGENETICS	ss5657762349	Oct 16, 2022 (156)
39	TOMMO_GENOMICS	ss5770763520	Oct 16, 2022 (156)
40	YY_MCH	ss5815446716	Oct 16, 2022 (156)
41	EVA	ss5828375025	Oct 16, 2022 (156)
42	EVA	ss5828375026	Oct 16, 2022 (156)
43	EVA	ss5851346696	Oct 16, 2022 (156)
44	1000Genomes	NC_000015.9 - 69225686	Oct 12, 2018 (152)
45	The Avon Longitudinal Study of Parents and Children Submission ignored due to conflicting rows: Row 37238809 (NC_000015.9:69225685::AC 208/3854) Row 37238810 (NC_000015.9:69225685:AC: 50/3854)	-	Oct 12, 2018 (152)
46	The Avon Longitudinal Study of Parents and Children Submission ignored due to conflicting rows: Row 37238809 (NC_000015.9:69225685::AC 208/3854) Row 37238810 (NC_000015.9:69225685:AC: 50/3854)	-	Oct 12, 2018 (152)
47	Genetic variation in the Estonian population	NC_000015.9 - 69225686	Oct 12, 2018 (152)
48	The Danish reference pan genome	NC_000015.9 - 69225686	Apr 27, 2020 (154)
49	gnomAD - Genomes Submission ignored due to conflicting rows: Row 472778806 (NC_000015.10:68933346::AC 9450/139866) Row 472778807 (NC_000015.10:68933346:AC: 1/139898)	-	Apr 26, 2021 (155)
50	gnomAD - Genomes Submission ignored due to conflicting rows: Row 472778806 (NC_000015.10:68933346::AC 9450/139866) Row 472778807 (NC_000015.10:68933346:AC: 1/139898)	-	Apr 26, 2021 (155)
51	Genome of the Netherlands Release 5	NC_000015.9 - 69225686	Apr 27, 2020 (154)
52	Korean Genome Project	NC_000015.10 - 68933347	Apr 27, 2020 (154)
53	Northern Sweden	NC_000015.9 - 69225686	Jul 13, 2019 (153)
54	8.3KJPN	NC_000015.9 - 69225686	Apr 26, 2021 (155)
55	14KJPN	NC_000015.10 - 68933347	Oct 16, 2022 (156)
56	TopMed	NC_000015.10 - 68933347	Apr 26, 2021 (155)
57	UK 10K study - Twins Submission ignored due to conflicting rows: Row 37238809 (NC_000015.9:69225685::AC 172/3708) Row 37238810 (NC_000015.9:69225685:AC: 42/3708)	-	Oct 12, 2018 (152)
58	UK 10K study - Twins Submission ignored due to conflicting rows: Row 37238809 (NC_000015.9:69225685::AC 172/3708) Row 37238810 (NC_000015.9:69225685:AC: 42/3708)	-	Oct 12, 2018 (152)
59	A Vietnamese Genetic Variation Database	NC_000015.9 - 69225686	Jul 13, 2019 (153)
60	ALFA	NC_000015.10 - 68933347	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).

Associated ID	History Updated (Build)
rs372209837	May 15, 2013 (138)
rs796179717	Nov 08, 2017 (151)

Added to this RefSNP Cluster:

Submission IDs	Observation SPDI	Canonical SPDI	Source RSIDs
ss1708343588, ss1708343593, ss5511472960, ss5828375026	NC_000015.9:69225685:AC:	NC_000015.10:68933346:ACACACACACAC… NC_000015.10:68933346:ACACACACACACA:ACACACACACA	(self)
ss3698144344, ss4290991000	NC_000015.10:68933346:AC:	NC_000015.10:68933346:ACACACACACAC… NC_000015.10:68933346:ACACACACACACA:ACACACACACA	(self)
27344387	NC_000015.10:68933346:ACACACACACAC… NC_000015.10:68933346:ACACACACACACA:ACACACACACA	NC_000015.10:68933346:ACACACACACAC… NC_000015.10:68933346:ACACACACACACA:ACACACACACA	(self)
ss289264916, ss327681449, ss327798453, ss328169826, ss552428518, ss552752833, ss553578150	NC_000015.8:67012739::AC	NC_000015.10:68933346:ACACACACACAC… NC_000015.10:68933346:ACACACACACACA:ACACACACACACACA	(self)
ss289264917	NC_000015.8:67012752::CA	NC_000015.10:68933346:ACACACACACAC… NC_000015.10:68933346:ACACACACACACA:ACACACACACACACA	(self)
67061624, 26372882, 497056, 16621308, 14318754, 74752294, 8283142, ss664283834, ss991916535, ss1375048854, ss1574877635, ss1968139335, ss2031273102, ss2628716395, ss3013487745, ss3680634634, ss3741033889, ss3840749744, ss5216782987, ss5657762349, ss5828375025	NC_000015.9:69225685::AC	NC_000015.10:68933346:ACACACACACAC… NC_000015.10:68933346:ACACACACACACA:ACACACACACACACA	(self)
ss1710673517, ss1710673518	NC_000015.9:69225687::AC	NC_000015.10:68933346:ACACACACACAC… NC_000015.10:68933346:ACACACACACACA:ACACACACACACACA	(self)
ss564017449	NC_000015.9:69225698::CA	NC_000015.10:68933346:ACACACACACAC… NC_000015.10:68933346:ACACACACACACA:ACACACACACACACA	(self)
32774223, 104600624, 211383043, ss3818556073, ss3846239235, ss3976396222, ss4290990999, ss4995837383, ss5298885979, ss5492572052, ss5770763520, ss5815446716, ss5851346696	NC_000015.10:68933346::AC	NC_000015.10:68933346:ACACACACACAC… NC_000015.10:68933346:ACACACACACACA:ACACACACACACACA	(self)
27344387	NC_000015.10:68933346:ACACACACACAC… NC_000015.10:68933346:ACACACACACACA:ACACACACACACACA	NC_000015.10:68933346:ACACACACACAC… NC_000015.10:68933346:ACACACACACACA:ACACACACACACACA	(self)
ss3698144343	NC_000015.10:68933348::AC	NC_000015.10:68933346:ACACACACACAC… NC_000015.10:68933346:ACACACACACACA:ACACACACACACACA	(self)
ss103834044	NT_010194.17:40016255::CA	NC_000015.10:68933346:ACACACACACAC… NC_000015.10:68933346:ACACACACACACA:ACACACACACACACA	(self)
27344387	NC_000015.10:68933346:ACACACACACAC… NC_000015.10:68933346:ACACACACACACA:ACACACACACACACACA	NC_000015.10:68933346:ACACACACACAC… NC_000015.10:68933346:ACACACACACACA:ACACACACACACACACA	(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 rs78616268

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

rs78616268