Name: rs118139980
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.

rs118139980

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr20:51759014 (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>C / T>G
Variation Type: SNV Single Nucleotide Variation
Frequency: C=0.003128 (828/264690, TOPMED)
C=0.003146 (441/140190, GnomAD)
C=0.00276 (53/19190, ALFA) (+ 9 more)
C=0.0012 (8/6404, 1000G_30x)
C=0.0016 (8/5008, 1000G)
C=0.0009 (4/4480, Estonian)
C=0.0042 (16/3854, ALSPAC)
C=0.0040 (15/3708, TWINSUK)
C=0.005 (5/998, GoNL)
C=0.002 (1/600, NorthernSweden)
C=0.2 (1/4, SGDP_PRJ)
G=0.2 (1/4, SGDP_PRJ)

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	19190	T=0.99724	C=0.00276
European	Sub	14286	T=0.99636	C=0.00364
African	Sub	2970	T=1.0000	C=0.0000
African Others	Sub	114	T=1.000	C=0.000
African American	Sub	2856	T=1.0000	C=0.0000
Asian	Sub	116	T=1.000	C=0.000
East Asian	Sub	88	T=1.00	C=0.00
Other Asian	Sub	28	T=1.00	C=0.00
Latin American 1	Sub	154	T=1.000	C=0.000
Latin American 2	Sub	616	T=0.998	C=0.002
South Asian	Sub	98	T=1.00	C=0.00
Other	Sub	950	T=1.000	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
TopMed	Global	Study-wide	264690	T=0.996872	C=0.003128
gnomAD - Genomes	Global	Study-wide	140190	T=0.996854	C=0.003146
gnomAD - Genomes	European	Sub	75942	T=0.99639	C=0.00361
gnomAD - Genomes	African	Sub	42006	T=0.99929	C=0.00071
gnomAD - Genomes	American	Sub	13640	T=0.99831	C=0.00169
gnomAD - Genomes	Ashkenazi Jewish	Sub	3318	T=0.9687	C=0.0313
gnomAD - Genomes	East Asian	Sub	3132	T=1.0000	C=0.0000
gnomAD - Genomes	Other	Sub	2152	T=0.9954	C=0.0046
Allele Frequency Aggregator	Total	Global	19190	T=0.99724	C=0.00276
Allele Frequency Aggregator	European	Sub	14286	T=0.99636	C=0.00364
Allele Frequency Aggregator	African	Sub	2970	T=1.0000	C=0.0000
Allele Frequency Aggregator	Other	Sub	950	T=1.000	C=0.000
Allele Frequency Aggregator	Latin American 2	Sub	616	T=0.998	C=0.002
Allele Frequency Aggregator	Latin American 1	Sub	154	T=1.000	C=0.000
Allele Frequency Aggregator	Asian	Sub	116	T=1.000	C=0.000
Allele Frequency Aggregator	South Asian	Sub	98	T=1.00	C=0.00
1000Genomes_30x	Global	Study-wide	6404	T=0.9988	C=0.0012
1000Genomes_30x	African	Sub	1786	T=1.0000	C=0.0000
1000Genomes_30x	Europe	Sub	1266	T=0.9961	C=0.0039
1000Genomes_30x	South Asian	Sub	1202	T=1.0000	C=0.0000
1000Genomes_30x	East Asian	Sub	1170	T=1.0000	C=0.0000
1000Genomes_30x	American	Sub	980	T=0.997	C=0.003
1000Genomes	Global	Study-wide	5008	T=0.9984	C=0.0016
1000Genomes	African	Sub	1322	T=1.0000	C=0.0000
1000Genomes	East Asian	Sub	1008	T=1.0000	C=0.0000
1000Genomes	Europe	Sub	1006	T=0.9950	C=0.0050
1000Genomes	South Asian	Sub	978	T=1.000	C=0.000
1000Genomes	American	Sub	694	T=0.996	C=0.004
Genetic variation in the Estonian population	Estonian	Study-wide	4480	T=0.9991	C=0.0009
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	T=0.9958	C=0.0042
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	T=0.9960	C=0.0040
Genome of the Netherlands Release 5	Genome of the Netherlands	Study-wide	998	T=0.995	C=0.005
Northern Sweden	ACPOP	Study-wide	600	T=0.998	C=0.002
SGDP_PRJ	Global	Study-wide	4	T=0.5	C=0.2, G=0.2

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.51759014T>C
GRCh38.p14 chr 20	NC_000020.11:g.51759014T>G
GRCh37.p13 chr 20	NC_000020.10:g.50375553T>C
GRCh37.p13 chr 20	NC_000020.10:g.50375553T>G

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

Molecule type	Change	Amino acid[Codon]	SO Term
ATP9A transcript	NM_006045.3:c.68+9288A>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	T=	C	G
GRCh38.p14 chr 20	NC_000020.11:g.51759014=	NC_000020.11:g.51759014T>C	NC_000020.11:g.51759014T>G
GRCh37.p13 chr 20	NC_000020.10:g.50375553=	NC_000020.10:g.50375553T>C	NC_000020.10:g.50375553T>G
ATP9A transcript	NM_006045.1:c.68+9288=	NM_006045.1:c.68+9288A>G	NM_006045.1:c.68+9288A>C
ATP9A transcript	NM_006045.3:c.68+9288=	NM_006045.3:c.68+9288A>G	NM_006045.3:c.68+9288A>C

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#.

26 SubSNP, 11 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	1000GENOMES	ss237862244	Jul 15, 2010 (132)
2	ILLUMINA	ss535870539	Sep 08, 2015 (146)
3	EVA-GONL	ss994809311	Aug 21, 2014 (142)
4	JMKIDD_LAB	ss1082267612	Aug 21, 2014 (142)
5	1000GENOMES	ss1365118677	Aug 21, 2014 (142)
6	EVA_UK10K_ALSPAC	ss1638964977	Apr 01, 2015 (144)
7	EVA_UK10K_TWINSUK	ss1681959010	Apr 01, 2015 (144)
8	EVA_DECODE	ss1698871352	Apr 01, 2015 (144)
9	HUMAN_LONGEVITY	ss2243466148	Dec 20, 2016 (150)
10	GNOMAD	ss2968403452	Nov 08, 2017 (151)
11	SWEGEN	ss3018323060	Nov 08, 2017 (151)
12	ILLUMINA	ss3628413362	Oct 12, 2018 (152)
13	EGCUT_WGS	ss3685006924	Jul 13, 2019 (153)
14	EVA_DECODE	ss3707120754	Jul 13, 2019 (153)
15	ACPOP	ss3743467361	Jul 13, 2019 (153)
16	EVA	ss3835715074	Apr 27, 2020 (154)
17	SGDP_PRJ	ss3889283864	Apr 27, 2020 (154)
18	TOPMED	ss5091610894	Apr 27, 2021 (155)
19	1000G_HIGH_COVERAGE	ss5309107191	Oct 13, 2022 (156)
20	EVA	ss5437967062	Oct 13, 2022 (156)
21	HUGCELL_USP	ss5501355948	Oct 13, 2022 (156)
22	1000G_HIGH_COVERAGE	ss5615711632	Oct 13, 2022 (156)
23	SANFORD_IMAGENETICS	ss5663383639	Oct 13, 2022 (156)
24	EVA	ss5845812029	Oct 13, 2022 (156)
25	EVA	ss5923780923	Oct 13, 2022 (156)
26	EVA	ss5958309363	Oct 13, 2022 (156)
27	1000Genomes	NC_000020.10 - 50375553	Oct 12, 2018 (152)
28	1000Genomes_30x	NC_000020.11 - 51759014	Oct 13, 2022 (156)
29	The Avon Longitudinal Study of Parents and Children	NC_000020.10 - 50375553	Oct 12, 2018 (152)
30	Genetic variation in the Estonian population	NC_000020.10 - 50375553	Oct 12, 2018 (152)
31	gnomAD - Genomes	NC_000020.11 - 51759014	Apr 27, 2021 (155)
32	Genome of the Netherlands Release 5	NC_000020.10 - 50375553	Apr 27, 2020 (154)
33	Northern Sweden	NC_000020.10 - 50375553	Jul 13, 2019 (153)
34	SGDP_PRJ	NC_000020.10 - 50375553	Apr 27, 2020 (154)
35	TopMed	NC_000020.11 - 51759014	Apr 27, 2021 (155)
36	UK 10K study - Twins	NC_000020.10 - 50375553	Oct 12, 2018 (152)
37	ALFA	NC_000020.11 - 51759014	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
ss1698871352	NC_000020.9:49808959:T:C	NC_000020.11:51759013:T:C	(self)
78593844, 43510996, 30745172, 19379531, 16752226, 41300844, 43510996, ss237862244, ss535870539, ss994809311, ss1365118677, ss1638964977, ss1681959010, ss2968403452, ss3018323060, ss3628413362, ss3685006924, ss3743467361, ss3835715074, ss3889283864, ss5437967062, ss5663383639, ss5845812029, ss5958309363	NC_000020.10:50375552:T:C	NC_000020.11:51759013:T:C	(self)
103237567, 554366576, 366719839, 6686439934, ss2243466148, ss3707120754, ss5091610894, ss5309107191, ss5501355948, ss5615711632, ss5923780923	NC_000020.11:51759013:T:C	NC_000020.11:51759013:T:C	(self)
41300844, ss1082267612, ss3889283864	NC_000020.10:50375552:T:G	NC_000020.11:51759013:T:G	(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 rs118139980

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

rs118139980