Name: rs72689228
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.

rs72689228

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr15:25849343 (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: G>A
Variation Type: SNV Single Nucleotide Variation
Frequency: A=0.010469 (2771/264690, TOPMED)
A=0.011316 (1587/140248, GnomAD)
A=0.01466 (277/18890, ALFA) (+ 11 more)
A=0.0055 (35/6404, 1000G_30x)
A=0.0048 (24/5008, 1000G)
A=0.0205 (92/4480, Estonian)
A=0.0166 (64/3854, ALSPAC)
A=0.0162 (60/3708, TWINSUK)
A=0.021 (21/998, GoNL)
A=0.025 (15/600, NorthernSweden)
A=0.009 (2/216, Qatari)
A=0.03 (1/40, GENOME_DK)
G=0.5 (2/4, SGDP_PRJ)
A=0.5 (2/4, SGDP_PRJ)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: ATP10A : Intron Variant
MIR4715 : 2KB Upstream 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: 20230706150541

Population	Group	Sample Size	Ref Allele	Alt Allele
Total	Global	18890	G=0.98534	A=0.01466
European	Sub	14286	G=0.98208	A=0.01792
African	Sub	2946	G=0.9980	A=0.0020
African Others	Sub	114	G=1.000	A=0.000
African American	Sub	2832	G=0.9979	A=0.0021
Asian	Sub	112	G=1.000	A=0.000
East Asian	Sub	86	G=1.00	A=0.00
Other Asian	Sub	26	G=1.00	A=0.00
Latin American 1	Sub	146	G=1.000	A=0.000
Latin American 2	Sub	610	G=0.982	A=0.018
South Asian	Sub	98	G=1.00	A=0.00
Other	Sub	692	G=0.994	A=0.006

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	G=0.989531	A=0.010469
gnomAD - Genomes	Global	Study-wide	140248	G=0.988684	A=0.011316
gnomAD - Genomes	European	Sub	75950	G=0.98240	A=0.01760
gnomAD - Genomes	African	Sub	42026	G=0.99745	A=0.00255
gnomAD - Genomes	American	Sub	13662	G=0.99173	A=0.00827
gnomAD - Genomes	Ashkenazi Jewish	Sub	3322	G=0.9967	A=0.0033
gnomAD - Genomes	East Asian	Sub	3134	G=0.9994	A=0.0006
gnomAD - Genomes	Other	Sub	2154	G=0.9921	A=0.0079
Allele Frequency Aggregator	Total	Global	18890	G=0.98534	A=0.01466
Allele Frequency Aggregator	European	Sub	14286	G=0.98208	A=0.01792
Allele Frequency Aggregator	African	Sub	2946	G=0.9980	A=0.0020
Allele Frequency Aggregator	Other	Sub	692	G=0.994	A=0.006
Allele Frequency Aggregator	Latin American 2	Sub	610	G=0.982	A=0.018
Allele Frequency Aggregator	Latin American 1	Sub	146	G=1.000	A=0.000
Allele Frequency Aggregator	Asian	Sub	112	G=1.000	A=0.000
Allele Frequency Aggregator	South Asian	Sub	98	G=1.00	A=0.00
1000Genomes_30x	Global	Study-wide	6404	G=0.9945	A=0.0055
1000Genomes_30x	African	Sub	1786	G=1.0000	A=0.0000
1000Genomes_30x	Europe	Sub	1266	G=0.9818	A=0.0182
1000Genomes_30x	South Asian	Sub	1202	G=0.9958	A=0.0042
1000Genomes_30x	East Asian	Sub	1170	G=1.0000	A=0.0000
1000Genomes_30x	American	Sub	980	G=0.993	A=0.007
1000Genomes	Global	Study-wide	5008	G=0.9952	A=0.0048
1000Genomes	African	Sub	1322	G=1.0000	A=0.0000
1000Genomes	East Asian	Sub	1008	G=1.0000	A=0.0000
1000Genomes	Europe	Sub	1006	G=0.9841	A=0.0159
1000Genomes	South Asian	Sub	978	G=0.996	A=0.004
1000Genomes	American	Sub	694	G=0.994	A=0.006
Genetic variation in the Estonian population	Estonian	Study-wide	4480	G=0.9795	A=0.0205
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	G=0.9834	A=0.0166
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	G=0.9838	A=0.0162
Genome of the Netherlands Release 5	Genome of the Netherlands	Study-wide	998	G=0.979	A=0.021
Northern Sweden	ACPOP	Study-wide	600	G=0.975	A=0.025
Qatari	Global	Study-wide	216	G=0.991	A=0.009
The Danish reference pan genome	Danish	Study-wide	40	G=0.97	A=0.03
SGDP_PRJ	Global	Study-wide	4	G=0.5	A=0.5

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.25849343G>A
GRCh37.p13 chr 15	NC_000015.9:g.26094490G>A
ATP10A RefSeqGene	NG_009282.1:g.18860C>T

Gene: ATP10A, ATPase phospholipid transporting 10A (putative) (minus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
ATP10A transcript	NM_024490.4:c.449+13305C>T	N/A	Intron Variant
ATP10A transcript variant X2	XM_005268261.5:c.449+1330… XM_005268261.5:c.449+13305C>T	N/A	Intron Variant
ATP10A transcript variant X1	XM_011521826.3:c.449+1330… XM_011521826.3:c.449+13305C>T	N/A	Intron Variant
ATP10A transcript variant X3	XM_011521828.3:c.449+1330… XM_011521828.3:c.449+13305C>T	N/A	Intron Variant
ATP10A transcript variant X4	XM_017022437.2:c.-467+124… XM_017022437.2:c.-467+12439C>T	N/A	Intron Variant
ATP10A transcript variant X5	XM_047432890.1:c.-467+124… XM_047432890.1:c.-467+12439C>T	N/A	Intron Variant
ATP10A transcript variant X6	XM_047432891.1:c.-467+124… XM_047432891.1:c.-467+12439C>T	N/A	Intron Variant
ATP10A transcript variant X7	XM_011521829.3:c.	N/A	Genic Upstream Transcript Variant
ATP10A transcript variant X8	XM_047432892.1:c.	N/A	Genic Upstream Transcript Variant
ATP10A transcript variant X9	XR_001751368.2:n.	N/A	Intron Variant

Gene: MIR4715, microRNA 4715 (minus strand) : 2KB Upstream Variant

Molecule type	Change	Amino acid[Codon]	SO Term
MIR4715 transcript	NR_039865.1:n.	N/A	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	G=	A
GRCh38.p14 chr 15	NC_000015.10:g.25849343=	NC_000015.10:g.25849343G>A
GRCh37.p13 chr 15	NC_000015.9:g.26094490=	NC_000015.9:g.26094490G>A
ATP10A RefSeqGene	NG_009282.1:g.18860=	NG_009282.1:g.18860C>T
ATP10A transcript	NM_024490.3:c.449+13305=	NM_024490.3:c.449+13305C>T
ATP10A transcript	NM_024490.4:c.449+13305=	NM_024490.4:c.449+13305C>T
ATP10A transcript variant X1	XM_005268261.1:c.449+13305=	XM_005268261.1:c.449+13305C>T
ATP10A transcript variant X2	XM_005268261.5:c.449+13305=	XM_005268261.5:c.449+13305C>T
ATP10A transcript variant X1	XM_011521826.3:c.449+13305=	XM_011521826.3:c.449+13305C>T
ATP10A transcript variant X3	XM_011521828.3:c.449+13305=	XM_011521828.3:c.449+13305C>T
ATP10A transcript variant X4	XM_017022437.2:c.-467+12439=	XM_017022437.2:c.-467+12439C>T
ATP10A transcript variant X5	XM_047432890.1:c.-467+12439=	XM_047432890.1:c.-467+12439C>T
ATP10A transcript variant X6	XM_047432891.1:c.-467+12439=	XM_047432891.1:c.-467+12439C>T

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#.

27 SubSNP, 13 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	1000GENOMES	ss108680501	Feb 13, 2009 (130)
2	BCM-HGSC-SUB	ss207259491	Jul 04, 2010 (132)
3	1000GENOMES	ss338652069	May 09, 2011 (134)
4	EVA-GONL	ss991606991	Aug 21, 2014 (142)
5	1000GENOMES	ss1352753933	Aug 21, 2014 (142)
6	EVA_GENOME_DK	ss1577512962	Apr 01, 2015 (144)
7	EVA_UK10K_ALSPAC	ss1632636157	Apr 01, 2015 (144)
8	EVA_UK10K_TWINSUK	ss1675630190	Apr 01, 2015 (144)
9	EVA_DECODE	ss1695617714	Apr 01, 2015 (144)
10	WEILL_CORNELL_DGM	ss1935002987	Feb 12, 2016 (147)
11	HUMAN_LONGEVITY	ss2205392356	Dec 20, 2016 (150)
12	GNOMAD	ss2932805947	Nov 08, 2017 (151)
13	SWEGEN	ss3012980481	Nov 08, 2017 (151)
14	EGCUT_WGS	ss3680149472	Jul 13, 2019 (153)
15	EVA_DECODE	ss3697551611	Jul 13, 2019 (153)
16	ACPOP	ss3740772358	Jul 13, 2019 (153)
17	KHV_HUMAN_GENOMES	ss3818186784	Jul 13, 2019 (153)
18	EVA	ss3834147423	Apr 27, 2020 (154)
19	SGDP_PRJ	ss3882515827	Apr 27, 2020 (154)
20	TOPMED	ss4985162940	Apr 26, 2021 (155)
21	1000G_HIGH_COVERAGE	ss5297801010	Oct 16, 2022 (156)
22	EVA	ss5418086742	Oct 16, 2022 (156)
23	HUGCELL_USP	ss5491621324	Oct 16, 2022 (156)
24	1000G_HIGH_COVERAGE	ss5598882836	Oct 16, 2022 (156)
25	EVA	ss5827960278	Oct 16, 2022 (156)
26	EVA	ss5875181299	Oct 16, 2022 (156)
27	EVA	ss5948550222	Oct 16, 2022 (156)
28	1000Genomes	NC_000015.9 - 26094490	Oct 12, 2018 (152)
29	1000Genomes_30x	NC_000015.10 - 25849343	Oct 16, 2022 (156)
30	The Avon Longitudinal Study of Parents and Children	NC_000015.9 - 26094490	Oct 12, 2018 (152)
31	Genetic variation in the Estonian population	NC_000015.9 - 26094490	Oct 12, 2018 (152)
32	The Danish reference pan genome	NC_000015.9 - 26094490	Apr 27, 2020 (154)
33	gnomAD - Genomes	NC_000015.10 - 25849343	Apr 26, 2021 (155)
34	Genome of the Netherlands Release 5	NC_000015.9 - 26094490	Apr 27, 2020 (154)
35	Northern Sweden	NC_000015.9 - 26094490	Jul 13, 2019 (153)
36	Qatari	NC_000015.9 - 26094490	Apr 27, 2020 (154)
37	SGDP_PRJ	NC_000015.9 - 26094490	Apr 27, 2020 (154)
38	TopMed	NC_000015.10 - 25849343	Apr 26, 2021 (155)
39	UK 10K study - Twins	NC_000015.9 - 26094490	Oct 12, 2018 (152)
40	ALFA	NC_000015.10 - 25849343	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
ss108680501, ss207259491, ss1695617714	NC_000015.8:23645582:G:A	NC_000015.10:25849342:G:A	(self)
65798400, 36536523, 25887720, 3785257, 16321278, 14057223, 17044917, 34532807, 36536523, ss338652069, ss991606991, ss1352753933, ss1577512962, ss1632636157, ss1675630190, ss1935002987, ss2932805947, ss3012980481, ss3680149472, ss3740772358, ss3834147423, ss3882515827, ss5418086742, ss5827960278, ss5948550222	NC_000015.9:26094489:G:A	NC_000015.10:25849342:G:A	(self)
86408771, 463811588, 200708600, 7411074724, ss2205392356, ss3697551611, ss3818186784, ss4985162940, ss5297801010, ss5491621324, ss5598882836, ss5875181299	NC_000015.10:25849342:G:A	NC_000015.10:25849342:G:A	(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 rs72689228

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

rs72689228