Name: rs2306006
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.

rs2306006

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr4:42578440 (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: T>A / T>C
Variation Type: SNV Single Nucleotide Variation
Frequency: C=0.000257 (36/140216, GnomAD)
C=0.01334 (377/28258, 14KJPN)
C=0.01289 (216/16760, 8.3KJPN) (+ 7 more)
C=0.00007 (1/14414, ALFA)
C=0.0008 (5/6404, 1000G_30x)
C=0.0010 (5/5008, 1000G)
C=0.0212 (62/2922, KOREAN)
C=0.0186 (34/1832, Korea1K)
T=0.5 (1/2, SGDP_PRJ)
C=0.5 (1/2, SGDP_PRJ)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: ATP8A1 : 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: 20230706150541

Population	Group	Sample Size	Ref Allele	Alt Allele
Total	Global	14414	T=0.99993	A=0.00000, C=0.00007
European	Sub	9820	T=1.0000	A=0.0000, C=0.0000
African	Sub	2946	T=0.9997	A=0.0000, C=0.0003
African Others	Sub	114	T=1.000	A=0.000, C=0.000
African American	Sub	2832	T=0.9996	A=0.0000, C=0.0004
Asian	Sub	110	T=1.000	A=0.000, C=0.000
East Asian	Sub	84	T=1.00	A=0.00, C=0.00
Other Asian	Sub	26	T=1.00	A=0.00, C=0.00
Latin American 1	Sub	146	T=1.000	A=0.000, C=0.000
Latin American 2	Sub	610	T=1.000	A=0.000, C=0.000
South Asian	Sub	98	T=1.00	A=0.00, C=0.00
Other	Sub	684	T=1.000	A=0.000, C=0.000

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	140216	T=0.999743	C=0.000257
gnomAD - Genomes	European	Sub	75926	T=0.99992	C=0.00008
gnomAD - Genomes	African	Sub	42038	T=1.00000	C=0.00000
gnomAD - Genomes	American	Sub	13646	T=0.99985	C=0.00015
gnomAD - Genomes	Ashkenazi Jewish	Sub	3322	T=1.0000	C=0.0000
gnomAD - Genomes	East Asian	Sub	3132	T=0.9911	C=0.0089
gnomAD - Genomes	Other	Sub	2152	T=1.0000	C=0.0000
14KJPN	JAPANESE	Study-wide	28258	T=0.98666	C=0.01334
8.3KJPN	JAPANESE	Study-wide	16760	T=0.98711	C=0.01289
Allele Frequency Aggregator	Total	Global	14414	T=0.99993	A=0.00000, C=0.00007
Allele Frequency Aggregator	European	Sub	9820	T=1.0000	A=0.0000, C=0.0000
Allele Frequency Aggregator	African	Sub	2946	T=0.9997	A=0.0000, C=0.0003
Allele Frequency Aggregator	Other	Sub	684	T=1.000	A=0.000, C=0.000
Allele Frequency Aggregator	Latin American 2	Sub	610	T=1.000	A=0.000, C=0.000
Allele Frequency Aggregator	Latin American 1	Sub	146	T=1.000	A=0.000, C=0.000
Allele Frequency Aggregator	Asian	Sub	110	T=1.000	A=0.000, C=0.000
Allele Frequency Aggregator	South Asian	Sub	98	T=1.00	A=0.00, C=0.00
1000Genomes_30x	Global	Study-wide	6404	T=0.9992	C=0.0008
1000Genomes_30x	African	Sub	1786	T=1.0000	C=0.0000
1000Genomes_30x	Europe	Sub	1266	T=1.0000	C=0.0000
1000Genomes_30x	South Asian	Sub	1202	T=1.0000	C=0.0000
1000Genomes_30x	East Asian	Sub	1170	T=0.9957	C=0.0043
1000Genomes_30x	American	Sub	980	T=1.000	C=0.000
1000Genomes	Global	Study-wide	5008	T=0.9990	C=0.0010
1000Genomes	African	Sub	1322	T=1.0000	C=0.0000
1000Genomes	East Asian	Sub	1008	T=0.9950	C=0.0050
1000Genomes	Europe	Sub	1006	T=1.0000	C=0.0000
1000Genomes	South Asian	Sub	978	T=1.000	C=0.000
1000Genomes	American	Sub	694	T=1.000	C=0.000
KOREAN population from KRGDB	KOREAN	Study-wide	2922	T=0.9788	C=0.0212
Korean Genome Project	KOREAN	Study-wide	1832	T=0.9814	C=0.0186
SGDP_PRJ	Global	Study-wide	2	T=0.5	C=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 4	NC_000004.12:g.42578440T>A
GRCh38.p14 chr 4	NC_000004.12:g.42578440T>C
GRCh37.p13 chr 4	NC_000004.11:g.42580457T>A
GRCh37.p13 chr 4	NC_000004.11:g.42580457T>C

Gene: ATP8A1, ATPase phospholipid transporting 8A1 (minus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
ATP8A1 transcript variant 2	NM_001105529.1:c.1001-53A… NM_001105529.1:c.1001-53A>T	N/A	Intron Variant
ATP8A1 transcript variant 3	NM_001400024.1:c.1001-53A… NM_001400024.1:c.1001-53A>T	N/A	Intron Variant
ATP8A1 transcript variant 4	NM_001400025.1:c.1001-53A… NM_001400025.1:c.1001-53A>T	N/A	Intron Variant
ATP8A1 transcript variant 5	NM_001400026.1:c.1001-53A… NM_001400026.1:c.1001-53A>T	N/A	Intron Variant
ATP8A1 transcript variant 6	NM_001400027.1:c.509-53A>T	N/A	Intron Variant
ATP8A1 transcript variant 1	NM_006095.2:c.1001-53A>T	N/A	Intron Variant
ATP8A1 transcript variant X1	XM_011513615.2:c.1001-53A… XM_011513615.2:c.1001-53A>T	N/A	Intron Variant
ATP8A1 transcript variant X2	XM_011513616.3:c.1001-53A… XM_011513616.3:c.1001-53A>T	N/A	Intron Variant
ATP8A1 transcript variant X3	XM_047449508.1:c.1001-53A… XM_047449508.1:c.1001-53A>T	N/A	Intron Variant
ATP8A1 transcript variant X4	XM_047449509.1:c.509-53A>T	N/A	Intron Variant
ATP8A1 transcript variant X5	XM_047449510.1:c.1001-53A… XM_047449510.1:c.1001-53A>T	N/A	Intron Variant
ATP8A1 transcript variant X6	XM_047449511.1:c.1001-53A… XM_047449511.1:c.1001-53A>T	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	T=	A	C
GRCh38.p14 chr 4	NC_000004.12:g.42578440=	NC_000004.12:g.42578440T>A	NC_000004.12:g.42578440T>C
GRCh37.p13 chr 4	NC_000004.11:g.42580457=	NC_000004.11:g.42580457T>A	NC_000004.11:g.42580457T>C
ATP8A1 transcript variant 2	NM_001105529.1:c.1001-53=	NM_001105529.1:c.1001-53A>T	NM_001105529.1:c.1001-53A>G
ATP8A1 transcript variant 3	NM_001400024.1:c.1001-53=	NM_001400024.1:c.1001-53A>T	NM_001400024.1:c.1001-53A>G
ATP8A1 transcript variant 4	NM_001400025.1:c.1001-53=	NM_001400025.1:c.1001-53A>T	NM_001400025.1:c.1001-53A>G
ATP8A1 transcript variant 5	NM_001400026.1:c.1001-53=	NM_001400026.1:c.1001-53A>T	NM_001400026.1:c.1001-53A>G
ATP8A1 transcript variant 6	NM_001400027.1:c.509-53=	NM_001400027.1:c.509-53A>T	NM_001400027.1:c.509-53A>G
ATP8A1 transcript variant 1	NM_006095.2:c.1001-53=	NM_006095.2:c.1001-53A>T	NM_006095.2:c.1001-53A>G
ATP8A1 transcript variant X1	XM_005248043.1:c.1001-53=	XM_005248043.1:c.1001-53A>T	XM_005248043.1:c.1001-53A>G
ATP8A1 transcript variant X1	XM_011513615.2:c.1001-53=	XM_011513615.2:c.1001-53A>T	XM_011513615.2:c.1001-53A>G
ATP8A1 transcript variant X2	XM_011513616.3:c.1001-53=	XM_011513616.3:c.1001-53A>T	XM_011513616.3:c.1001-53A>G
ATP8A1 transcript variant X3	XM_047449508.1:c.1001-53=	XM_047449508.1:c.1001-53A>T	XM_047449508.1:c.1001-53A>G
ATP8A1 transcript variant X4	XM_047449509.1:c.509-53=	XM_047449509.1:c.509-53A>T	XM_047449509.1:c.509-53A>G
ATP8A1 transcript variant X5	XM_047449510.1:c.1001-53=	XM_047449510.1:c.1001-53A>T	XM_047449510.1:c.1001-53A>G
ATP8A1 transcript variant X6	XM_047449511.1:c.1001-53=	XM_047449511.1:c.1001-53A>T	XM_047449511.1:c.1001-53A>G

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#.

23 SubSNP, 11 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	YUSUKE	ss3253400	Sep 28, 2001 (100)
2	GMI	ss277672522	May 04, 2012 (137)
3	1000GENOMES	ss331584482	May 09, 2011 (134)
4	1000GENOMES	ss1309388863	Aug 21, 2014 (142)
5	HUMAN_LONGEVITY	ss2262371216	Dec 20, 2016 (150)
6	GRF	ss2705780823	Nov 08, 2017 (151)
7	GNOMAD	ss2808291765	Nov 08, 2017 (151)
8	EVA	ss3761699495	Jul 13, 2019 (153)
9	KHV_HUMAN_GENOMES	ss3804832061	Jul 13, 2019 (153)
10	SGDP_PRJ	ss3858730363	Apr 26, 2020 (154)
11	KRGDB	ss3904914154	Apr 26, 2020 (154)
12	KOGIC	ss3953970960	Apr 26, 2020 (154)
13	TOPMED	ss4610909100	Apr 26, 2021 (155)
14	TOPMED	ss4610909101	Apr 26, 2021 (155)
15	TOMMO_GENOMICS	ss5165264435	Apr 26, 2021 (155)
16	1000G_HIGH_COVERAGE	ss5258885671	Oct 13, 2022 (156)
17	EVA	ss5348424216	Oct 13, 2022 (156)
18	HUGCELL_USP	ss5457704129	Oct 13, 2022 (156)
19	1000G_HIGH_COVERAGE	ss5539762230	Oct 13, 2022 (156)
20	TOMMO_GENOMICS	ss5699207517	Oct 13, 2022 (156)
21	YY_MCH	ss5804976393	Oct 13, 2022 (156)
22	EVA	ss5863110935	Oct 13, 2022 (156)
23	EVA	ss5963233037	Oct 13, 2022 (156)
24	1000Genomes	NC_000004.11 - 42580457	Oct 12, 2018 (152)
25	1000Genomes_30x	NC_000004.12 - 42578440	Oct 13, 2022 (156)
26	gnomAD - Genomes	NC_000004.12 - 42578440	Apr 26, 2021 (155)
27	KOREAN population from KRGDB	NC_000004.11 - 42580457	Apr 26, 2020 (154)
28	Korean Genome Project	NC_000004.12 - 42578440	Apr 26, 2020 (154)
29	SGDP_PRJ	NC_000004.11 - 42580457	Apr 26, 2020 (154)
30	8.3KJPN	NC_000004.11 - 42580457	Apr 26, 2021 (155)
31	14KJPN	NC_000004.12 - 42578440	Oct 13, 2022 (156)
32	TopMed Submission ignored due to conflicting rows: Row 448286656 (NC_000004.12:42578439:T:A 1/264690) Row 448286657 (NC_000004.12:42578439:T:C 74/264690)	-	Apr 26, 2021 (155)
33	TopMed Submission ignored due to conflicting rows: Row 448286656 (NC_000004.12:42578439:T:A 1/264690) Row 448286657 (NC_000004.12:42578439:T:C 74/264690)	-	Apr 26, 2021 (155)
34	ALFA	NC_000004.12 - 42578440	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
8572095938, ss4610909100	NC_000004.12:42578439:T:A	NC_000004.12:42578439:T:A	(self)
ss277672522	NC_000004.10:42275213:T:C	NC_000004.12:42578439:T:C	(self)
20772646, 12091548, 10747343, 23233742, ss331584482, ss1309388863, ss2705780823, ss2808291765, ss3761699495, ss3858730363, ss3904914154, ss5165264435, ss5348424216, ss5963233037	NC_000004.11:42580456:T:C	NC_000004.12:42578439:T:C	(self)
27288165, 147063641, 10348961, 33044621, 8572095938, ss2262371216, ss3804832061, ss3953970960, ss4610909101, ss5258885671, ss5457704129, ss5539762230, ss5699207517, ss5804976393, ss5863110935	NC_000004.12:42578439:T:C	NC_000004.12:42578439:T:C	(self)
ss3253400	NT_006238.11:2283360:T:C	NC_000004.12:42578439:T:C	(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 rs2306006

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
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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

rs2306006