Name: rs35031713
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.

rs35031713

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr20:51730105 (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>C
Variation Type: SNV Single Nucleotide Variation
Frequency: C=0.087548 (23173/264690, TOPMED)
C=0.087996 (12330/140120, GnomAD)
C=0.08502 (1606/18890, ALFA) (+ 14 more)
C=0.0801 (513/6404, 1000G_30x)
C=0.0761 (381/5008, 1000G)
C=0.0781 (350/4480, Estonian)
C=0.0817 (315/3854, ALSPAC)
C=0.0728 (270/3708, TWINSUK)
C=0.0003 (1/2922, KOREAN)
C=0.075 (75/998, GoNL)
C=0.053 (32/600, NorthernSweden)
C=0.019 (4/216, Qatari)
C=0.005 (1/216, Vietnamese)
G=0.48 (31/64, SGDP_PRJ)
C=0.12 (5/40, GENOME_DK)
G=0.5 (1/2, Siberian)
C=0.5 (1/2, Siberian)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: ATP9A : 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	18890	G=0.91498	C=0.08502
European	Sub	14286	G=0.92377	C=0.07623
African	Sub	2946	G=0.8629	C=0.1371
African Others	Sub	114	G=0.895	C=0.105
African American	Sub	2832	G=0.8616	C=0.1384
Asian	Sub	112	G=1.000	C=0.000
East Asian	Sub	86	G=1.00	C=0.00
Other Asian	Sub	26	G=1.00	C=0.00
Latin American 1	Sub	146	G=0.911	C=0.089
Latin American 2	Sub	610	G=0.956	C=0.044
South Asian	Sub	98	G=0.95	C=0.05
Other	Sub	692	G=0.902	C=0.098

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=0.912452	C=0.087548
gnomAD - Genomes	Global	Study-wide	140120	G=0.912004	C=0.087996
gnomAD - Genomes	European	Sub	75900	G=0.92783	C=0.07217
gnomAD - Genomes	African	Sub	41978	G=0.86109	C=0.13891
gnomAD - Genomes	American	Sub	13638	G=0.95131	C=0.04869
gnomAD - Genomes	Ashkenazi Jewish	Sub	3322	G=0.9395	C=0.0605
gnomAD - Genomes	East Asian	Sub	3128	G=0.9984	C=0.0016
gnomAD - Genomes	Other	Sub	2154	G=0.9299	C=0.0701
Allele Frequency Aggregator	Total	Global	18890	G=0.91498	C=0.08502
Allele Frequency Aggregator	European	Sub	14286	G=0.92377	C=0.07623
Allele Frequency Aggregator	African	Sub	2946	G=0.8629	C=0.1371
Allele Frequency Aggregator	Other	Sub	692	G=0.902	C=0.098
Allele Frequency Aggregator	Latin American 2	Sub	610	G=0.956	C=0.044
Allele Frequency Aggregator	Latin American 1	Sub	146	G=0.911	C=0.089
Allele Frequency Aggregator	Asian	Sub	112	G=1.000	C=0.000
Allele Frequency Aggregator	South Asian	Sub	98	G=0.95	C=0.05
1000Genomes_30x	Global	Study-wide	6404	G=0.9199	C=0.0801
1000Genomes_30x	African	Sub	1786	G=0.8315	C=0.1685
1000Genomes_30x	Europe	Sub	1266	G=0.9202	C=0.0798
1000Genomes_30x	South Asian	Sub	1202	G=0.9459	C=0.0541
1000Genomes_30x	East Asian	Sub	1170	G=1.0000	C=0.0000
1000Genomes_30x	American	Sub	980	G=0.953	C=0.047
1000Genomes	Global	Study-wide	5008	G=0.9239	C=0.0761
1000Genomes	African	Sub	1322	G=0.8313	C=0.1687
1000Genomes	East Asian	Sub	1008	G=1.0000	C=0.0000
1000Genomes	Europe	Sub	1006	G=0.9254	C=0.0746
1000Genomes	South Asian	Sub	978	G=0.951	C=0.049
1000Genomes	American	Sub	694	G=0.950	C=0.050
Genetic variation in the Estonian population	Estonian	Study-wide	4480	G=0.9219	C=0.0781
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	G=0.9183	C=0.0817
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	G=0.9272	C=0.0728
KOREAN population from KRGDB	KOREAN	Study-wide	2922	G=0.9997	C=0.0003
Genome of the Netherlands Release 5	Genome of the Netherlands	Study-wide	998	G=0.925	C=0.075
Northern Sweden	ACPOP	Study-wide	600	G=0.947	C=0.053
Qatari	Global	Study-wide	216	G=0.981	C=0.019
A Vietnamese Genetic Variation Database	Global	Study-wide	216	G=0.995	C=0.005
SGDP_PRJ	Global	Study-wide	64	G=0.48	C=0.52
The Danish reference pan genome	Danish	Study-wide	40	G=0.88	C=0.12
Siberian	Global	Study-wide	2	G=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 20	NC_000020.11:g.51730105G>C
GRCh37.p13 chr 20	NC_000020.10:g.50346644G>C

Gene: ATP9A, ATPase phospholipid transporting 9A (putative) (minus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
ATP9A transcript	NM_006045.3:c.69-127C>G	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	G=	C
GRCh38.p14 chr 20	NC_000020.11:g.51730105=	NC_000020.11:g.51730105G>C
GRCh37.p13 chr 20	NC_000020.10:g.50346644=	NC_000020.10:g.50346644G>C
ATP9A transcript	NM_006045.1:c.69-127=	NM_006045.1:c.69-127C>G
ATP9A transcript	NM_006045.3:c.69-127=	NM_006045.3:c.69-127C>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#.

45 SubSNP, 16 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	ABI	ss44200794	Mar 14, 2006 (126)
2	HUMANGENOME_JCVI	ss96234544	Feb 06, 2009 (130)
3	ILLUMINA-UK	ss117573575	Feb 14, 2009 (130)
4	ENSEMBL	ss135694550	Dec 01, 2009 (131)
5	1000GENOMES	ss228396374	Jul 14, 2010 (132)
6	1000GENOMES	ss237862127	Jul 15, 2010 (132)
7	PJP	ss292577700	May 09, 2011 (134)
8	TISHKOFF	ss566304468	Apr 25, 2013 (138)
9	EVA-GONL	ss994809009	Aug 21, 2014 (142)
10	JMKIDD_LAB	ss1082267390	Aug 21, 2014 (142)
11	1000GENOMES	ss1365117696	Aug 21, 2014 (142)
12	EVA_GENOME_DK	ss1579538721	Apr 01, 2015 (144)
13	EVA_UK10K_ALSPAC	ss1638964431	Apr 01, 2015 (144)
14	EVA_UK10K_TWINSUK	ss1681958464	Apr 01, 2015 (144)
15	EVA_DECODE	ss1698871013	Apr 01, 2015 (144)
16	HAMMER_LAB	ss1809540523	Sep 08, 2015 (146)
17	WEILL_CORNELL_DGM	ss1938325709	Feb 12, 2016 (147)
18	JJLAB	ss2029942486	Sep 14, 2016 (149)
19	USC_VALOUEV	ss2158512676	Dec 20, 2016 (150)
20	HUMAN_LONGEVITY	ss2243464147	Dec 20, 2016 (150)
21	GNOMAD	ss2968400748	Nov 08, 2017 (151)
22	SWEGEN	ss3018322591	Nov 08, 2017 (151)
23	BIOINF_KMB_FNS_UNIBA	ss3028804050	Nov 08, 2017 (151)
24	CSHL	ss3352549554	Nov 08, 2017 (151)
25	URBANLAB	ss3651037127	Oct 12, 2018 (152)
26	EGCUT_WGS	ss3685006466	Jul 13, 2019 (153)
27	EVA_DECODE	ss3707120213	Jul 13, 2019 (153)
28	ACPOP	ss3743467096	Jul 13, 2019 (153)
29	EVA	ss3758751236	Jul 13, 2019 (153)
30	PACBIO	ss3788670440	Jul 13, 2019 (153)
31	PACBIO	ss3793557759	Jul 13, 2019 (153)
32	PACBIO	ss3798444802	Jul 13, 2019 (153)
33	KHV_HUMAN_GENOMES	ss3821908249	Jul 13, 2019 (153)
34	SGDP_PRJ	ss3889283277	Apr 27, 2020 (154)
35	KRGDB	ss3939593717	Apr 27, 2020 (154)
36	TOPMED	ss5091603152	Apr 27, 2021 (155)
37	1000G_HIGH_COVERAGE	ss5309106255	Oct 13, 2022 (156)
38	EVA	ss5437965529	Oct 13, 2022 (156)
39	HUGCELL_USP	ss5501355035	Oct 13, 2022 (156)
40	EVA	ss5512241711	Oct 13, 2022 (156)
41	1000G_HIGH_COVERAGE	ss5615710318	Oct 13, 2022 (156)
42	SANFORD_IMAGENETICS	ss5663383071	Oct 13, 2022 (156)
43	EVA	ss5845811656	Oct 13, 2022 (156)
44	EVA	ss5923779930	Oct 13, 2022 (156)
45	EVA	ss5958308814	Oct 13, 2022 (156)
46	1000Genomes	NC_000020.10 - 50346644	Oct 12, 2018 (152)
47	1000Genomes_30x	NC_000020.11 - 51730105	Oct 13, 2022 (156)
48	The Avon Longitudinal Study of Parents and Children	NC_000020.10 - 50346644	Oct 12, 2018 (152)
49	Genetic variation in the Estonian population	NC_000020.10 - 50346644	Oct 12, 2018 (152)
50	The Danish reference pan genome	NC_000020.10 - 50346644	Apr 27, 2020 (154)
51	gnomAD - Genomes	NC_000020.11 - 51730105	Apr 27, 2021 (155)
52	Genome of the Netherlands Release 5	NC_000020.10 - 50346644	Apr 27, 2020 (154)
53	KOREAN population from KRGDB	NC_000020.10 - 50346644	Apr 27, 2020 (154)
54	Northern Sweden	NC_000020.10 - 50346644	Jul 13, 2019 (153)
55	Qatari	NC_000020.10 - 50346644	Apr 27, 2020 (154)
56	SGDP_PRJ	NC_000020.10 - 50346644	Apr 27, 2020 (154)
57	Siberian	NC_000020.10 - 50346644	Apr 27, 2020 (154)
58	TopMed	NC_000020.11 - 51730105	Apr 27, 2021 (155)
59	UK 10K study - Twins	NC_000020.10 - 50346644	Oct 12, 2018 (152)
60	A Vietnamese Genetic Variation Database	NC_000020.10 - 50346644	Jul 13, 2019 (153)
61	ALFA	NC_000020.11 - 51730105	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
ss117573575, ss292577700, ss1698871013	NC_000020.9:49780050:G:C	NC_000020.11:51730104:G:C	(self)
78592826, 43510391, 30744714, 5703660, 19379252, 46771111, 16751961, 20367631, 41300257, 11029030, 43510391, 9597588, ss228396374, ss237862127, ss566304468, ss994809009, ss1082267390, ss1365117696, ss1579538721, ss1638964431, ss1681958464, ss1809540523, ss1938325709, ss2029942486, ss2158512676, ss2968400748, ss3018322591, ss3352549554, ss3685006466, ss3743467096, ss3758751236, ss3788670440, ss3793557759, ss3798444802, ss3889283277, ss3939593717, ss5437965529, ss5512241711, ss5663383071, ss5845811656, ss5958308814	NC_000020.10:50346643:G:C	NC_000020.11:51730104:G:C	(self)
103236253, 554359904, 366712097, 5067992630, ss2243464147, ss3028804050, ss3651037127, ss3707120213, ss3821908249, ss5091603152, ss5309106255, ss5501355035, ss5615710318, ss5923779930	NC_000020.11:51730104:G:C	NC_000020.11:51730104:G:C	(self)
ss44200794, ss96234544, ss135694550	NT_011362.10:20542735:G:C	NC_000020.11:51730104:G: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 rs35031713

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

rs35031713