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dbSNP Short Genetic Variations

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.

rs150120594

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr13:25860369-25860372 (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
delAA / delA
Variation Type
Indel Insertion and Deletion
Frequency
delA=0.015520 (4108/264690, TOPMED)
delA=0.014079 (1974/140206, GnomAD)
delA=0.00947 (133/14050, ALFA) (+ 4 more)
delA=0.0172 (110/6404, 1000G_30x)
delA=0.0166 (83/5008, 1000G)
delA=0.0003 (1/3854, ALSPAC)
delA=0.0003 (1/3708, TWINSUK)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
ATP8A2 : 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 14050 AAAA=0.99053 AAA=0.00947
European Sub 9690 AAAA=0.9997 AAA=0.0003
African Sub 2898 AAAA=0.9589 AAA=0.0411
African Others Sub 114 AAAA=0.939 AAA=0.061
African American Sub 2784 AAAA=0.9598 AAA=0.0402
Asian Sub 112 AAAA=1.000 AAA=0.000
East Asian Sub 86 AAAA=1.00 AAA=0.00
Other Asian Sub 26 AAAA=1.00 AAA=0.00
Latin American 1 Sub 146 AAAA=0.986 AAA=0.014
Latin American 2 Sub 610 AAAA=0.997 AAA=0.003
South Asian Sub 98 AAAA=1.00 AAA=0.00
Other Sub 496 AAAA=0.986 AAA=0.014


Help

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").

Download
Study Population Group Sample Size Ref Allele Alt Allele
TopMed Global Study-wide 264690 (A)4=0.984480 delA=0.015520
gnomAD - Genomes Global Study-wide 140206 (A)4=0.985921 delA=0.014079
gnomAD - Genomes European Sub 75924 (A)4=0.99966 delA=0.00034
gnomAD - Genomes African Sub 42022 (A)4=0.95686 delA=0.04314
gnomAD - Genomes American Sub 13656 (A)4=0.99282 delA=0.00718
gnomAD - Genomes Ashkenazi Jewish Sub 3324 (A)4=0.9970 delA=0.0030
gnomAD - Genomes East Asian Sub 3130 (A)4=1.0000 delA=0.0000
gnomAD - Genomes Other Sub 2150 (A)4=0.9874 delA=0.0126
Allele Frequency Aggregator Total Global 14050 (A)4=0.99053 delA=0.00947
Allele Frequency Aggregator European Sub 9690 (A)4=0.9997 delA=0.0003
Allele Frequency Aggregator African Sub 2898 (A)4=0.9589 delA=0.0411
Allele Frequency Aggregator Latin American 2 Sub 610 (A)4=0.997 delA=0.003
Allele Frequency Aggregator Other Sub 496 (A)4=0.986 delA=0.014
Allele Frequency Aggregator Latin American 1 Sub 146 (A)4=0.986 delA=0.014
Allele Frequency Aggregator Asian Sub 112 (A)4=1.000 delA=0.000
Allele Frequency Aggregator South Asian Sub 98 (A)4=1.00 delA=0.00
1000Genomes_30x Global Study-wide 6404 (A)4=0.9828 delA=0.0172
1000Genomes_30x African Sub 1786 (A)4=0.9434 delA=0.0566
1000Genomes_30x Europe Sub 1266 (A)4=0.9992 delA=0.0008
1000Genomes_30x South Asian Sub 1202 (A)4=1.0000 delA=0.0000
1000Genomes_30x East Asian Sub 1170 (A)4=1.0000 delA=0.0000
1000Genomes_30x American Sub 980 (A)4=0.992 delA=0.008
1000Genomes Global Study-wide 5008 (A)4=0.9834 delA=0.0166
1000Genomes African Sub 1322 (A)4=0.9425 delA=0.0575
1000Genomes East Asian Sub 1008 (A)4=1.0000 delA=0.0000
1000Genomes Europe Sub 1006 (A)4=0.9990 delA=0.0010
1000Genomes South Asian Sub 978 (A)4=1.000 delA=0.000
1000Genomes American Sub 694 (A)4=0.991 delA=0.009
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 (A)4=0.9997 delA=0.0003
UK 10K study - Twins TWIN COHORT Study-wide 3708 (A)4=0.9997 delA=0.0003
Help

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 13 NC_000013.11:g.25860371_25860372del
GRCh38.p14 chr 13 NC_000013.11:g.25860372del
GRCh37.p13 chr 13 NC_000013.10:g.26434509_26434510del
GRCh37.p13 chr 13 NC_000013.10:g.26434510del
ATP8A2 RefSeqGene NG_042855.1:g.493361_493362del
ATP8A2 RefSeqGene NG_042855.1:g.493362del
Gene: ATP8A2, ATPase phospholipid transporting 8A2 (plus strand)
Molecule type Change Amino acid[Codon] SO Term
ATP8A2 transcript variant 2 NM_001313741.1:c.2823+115…

NM_001313741.1:c.2823+115_2823+116del

N/A Intron Variant
ATP8A2 transcript variant 1 NM_016529.6:c.3018+115_30…

NM_016529.6:c.3018+115_3018+116del

N/A Intron Variant
ATP8A2 transcript variant X1 XM_005266419.2:c.2898+115…

XM_005266419.2:c.2898+115_2898+116del

N/A Intron Variant
ATP8A2 transcript variant X1 XM_011535103.2:c.2943+115…

XM_011535103.2:c.2943+115_2943+116del

N/A Intron Variant
ATP8A2 transcript variant X2 XM_011535104.3:c.2898+115…

XM_011535104.3:c.2898+115_2898+116del

N/A Intron Variant
ATP8A2 transcript variant X5 XM_011535106.2:c.3018+115…

XM_011535106.2:c.3018+115_3018+116del

N/A Intron Variant
ATP8A2 transcript variant X4 XM_011535107.4:c.3018+115…

XM_011535107.4:c.3018+115_3018+116del

N/A Intron Variant
ATP8A2 transcript variant X5 XM_011535109.4:c.2538+115…

XM_011535109.4:c.2538+115_2538+116del

N/A Intron Variant
ATP8A2 transcript variant X6 XM_024449369.1:c.2424+115…

XM_024449369.1:c.2424+115_2424+116del

N/A Intron Variant
ATP8A2 transcript variant X3 XM_047430383.1:c.2898+115…

XM_047430383.1:c.2898+115_2898+116del

N/A Intron Variant
ATP8A2 transcript variant X7 XM_011535113.3:c. N/A Genic Downstream Transcript Variant
ATP8A2 transcript variant X8 XM_017020625.3:c. N/A Genic Downstream Transcript Variant
ATP8A2 transcript variant X9 XM_017020626.2:c. N/A Genic Downstream Transcript Variant
Help

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
Help

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 (A)4= delAA delA
GRCh38.p14 chr 13 NC_000013.11:g.25860369_25860372= NC_000013.11:g.25860371_25860372del NC_000013.11:g.25860372del
GRCh37.p13 chr 13 NC_000013.10:g.26434507_26434510= NC_000013.10:g.26434509_26434510del NC_000013.10:g.26434510del
ATP8A2 RefSeqGene NG_042855.1:g.493359_493362= NG_042855.1:g.493361_493362del NG_042855.1:g.493362del
ATP8A2 transcript variant 2 NM_001313741.1:c.2823+113= NM_001313741.1:c.2823+115_2823+116del NM_001313741.1:c.2823+116del
ATP8A2 transcript NM_016529.4:c.3018+113= NM_016529.4:c.3018+115_3018+116del NM_016529.4:c.3018+116del
ATP8A2 transcript variant 1 NM_016529.6:c.3018+113= NM_016529.6:c.3018+115_3018+116del NM_016529.6:c.3018+116del
ATP8A2 transcript variant X2 XM_005266419.1:c.2898+113= XM_005266419.1:c.2898+115_2898+116del XM_005266419.1:c.2898+116del
ATP8A2 transcript variant X1 XM_005266419.2:c.2898+113= XM_005266419.2:c.2898+115_2898+116del XM_005266419.2:c.2898+116del
ATP8A2 transcript variant X2 XM_005266420.1:c.2823+113= XM_005266420.1:c.2823+115_2823+116del XM_005266420.1:c.2823+116del
ATP8A2 transcript variant X1 XM_011535103.2:c.2943+113= XM_011535103.2:c.2943+115_2943+116del XM_011535103.2:c.2943+116del
ATP8A2 transcript variant X2 XM_011535104.3:c.2898+113= XM_011535104.3:c.2898+115_2898+116del XM_011535104.3:c.2898+116del
ATP8A2 transcript variant X5 XM_011535106.2:c.3018+113= XM_011535106.2:c.3018+115_3018+116del XM_011535106.2:c.3018+116del
ATP8A2 transcript variant X4 XM_011535107.4:c.3018+113= XM_011535107.4:c.3018+115_3018+116del XM_011535107.4:c.3018+116del
ATP8A2 transcript variant X5 XM_011535109.4:c.2538+113= XM_011535109.4:c.2538+115_2538+116del XM_011535109.4:c.2538+116del
ATP8A2 transcript variant X6 XM_024449369.1:c.2424+113= XM_024449369.1:c.2424+115_2424+116del XM_024449369.1:c.2424+116del
ATP8A2 transcript variant X3 XM_047430383.1:c.2898+113= XM_047430383.1:c.2898+115_2898+116del XM_047430383.1:c.2898+116del
Help

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#.

20 SubSNP, 7 Frequency submissions
No Submitter Submission ID Date (Build)
1 1000GENOMES ss328055055 May 09, 2011 (134)
2 1000GENOMES ss499929018 May 04, 2012 (137)
3 LUNTER ss552577015 Apr 25, 2013 (138)
4 TISHKOFF ss554692225 Apr 25, 2013 (138)
5 WARNICH_LAB ss678392447 Apr 25, 2013 (138)
6 1000GENOMES ss1372931239 Aug 21, 2014 (142)
7 EVA_UK10K_ALSPAC ss1707716753 Apr 01, 2015 (144)
8 EVA_UK10K_TWINSUK ss1707716825 Apr 01, 2015 (144)
9 HAMMER_LAB ss1807531192 Sep 08, 2015 (146)
10 GNOMAD ss2917717475 Nov 08, 2017 (151)
11 KHV_HUMAN_GENOMES ss3816580906 Jul 13, 2019 (153)
12 FSA-LAB ss3984044152 Apr 26, 2021 (155)
13 EVA ss3986597405 Apr 26, 2021 (155)
14 TOPMED ss4940304936 Apr 26, 2021 (155)
15 1000G_HIGH_COVERAGE ss5293135400 Oct 16, 2022 (156)
16 HUGCELL_USP ss5487557636 Oct 16, 2022 (156)
17 1000G_HIGH_COVERAGE ss5591787161 Oct 16, 2022 (156)
18 SANFORD_IMAGENETICS ss5654424413 Oct 16, 2022 (156)
19 EVA ss5924413197 Oct 16, 2022 (156)
20 EVA ss5945828898 Oct 16, 2022 (156)
21 1000Genomes NC_000013.10 - 26434507 Oct 12, 2018 (152)
22 1000Genomes_30x NC_000013.11 - 25860369 Oct 16, 2022 (156)
23 The Avon Longitudinal Study of Parents and Children NC_000013.10 - 26434507 Oct 12, 2018 (152)
24 gnomAD - Genomes NC_000013.11 - 25860369 Apr 26, 2021 (155)
25 TopMed NC_000013.11 - 25860369 Apr 26, 2021 (155)
26 UK 10K study - Twins NC_000013.10 - 26434507 Oct 12, 2018 (152)
27 ALFA NC_000013.11 - 25860369 Apr 26, 2021 (155)
Help

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)
rs376118058 May 15, 2013 (138)
Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
ss3984044152 NC_000013.10:26434506:AA: NC_000013.11:25860368:AAAA:AA (self)
ss328055055, ss552577015 NC_000013.9:25332506:A: NC_000013.11:25860368:AAAA:AAA (self)
60382789, 33533930, 33533930, ss499929018, ss678392447, ss1372931239, ss1707716753, ss1707716825, ss1807531192, ss2917717475, ss3986597405, ss5654424413, ss5945828898 NC_000013.10:26434506:A: NC_000013.11:25860368:AAAA:AAA (self)
ss554692225 NC_000013.10:26434509:A: NC_000013.11:25860368:AAAA:AAA (self)
79313096, 425807881, 155850594, ss3816580906, ss4940304936, ss5293135400, ss5487557636, ss5591787161, ss5924413197 NC_000013.11:25860368:A: NC_000013.11:25860368:AAAA:AAA (self)
3387274828 NC_000013.11:25860368:AAAA:AAA NC_000013.11:25860368:AAAA:AAA (self)
Help

Publications tab displays PubMed articles citing the variation as a listing of PMID, Title, Author, Year, Journal, ordered by Year, descending.

No publications for rs150120594

Help

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.

Software version is: 2.0.1.post761+d5e8e07