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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.

rs59622418

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr4:42600983-42600984 (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
delT / dupT
Variation Type
Indel Insertion and Deletion
Frequency
delT=0.177336 (46939/264690, TOPMED)
delT=0.181846 (25266/138942, GnomAD)
delT=0.18726 (3468/18520, ALFA) (+ 8 more)
delT=0.1615 (1034/6404, 1000G_30x)
delT=0.1625 (814/5008, 1000G)
delT=0.2013 (902/4480, Estonian)
delT=0.2154 (830/3854, ALSPAC)
delT=0.2217 (822/3708, TWINSUK)
delT=0.225 (225/998, GoNL)
delT=0.185 (111/600, NorthernSweden)
delT=0.38 (15/40, GENOME_DK)
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 18520 TT=0.81274 T=0.18726
European Sub 14152 TT=0.79593 T=0.20407
African Sub 2898 TT=0.8816 T=0.1184
African Others Sub 114 TT=0.939 T=0.061
African American Sub 2784 TT=0.8793 T=0.1207
Asian Sub 112 TT=0.795 T=0.205
East Asian Sub 86 TT=0.78 T=0.22
Other Asian Sub 26 TT=0.85 T=0.15
Latin American 1 Sub 146 TT=0.822 T=0.178
Latin American 2 Sub 610 TT=0.851 T=0.149
South Asian Sub 98 TT=0.86 T=0.14
Other Sub 504 TT=0.835 T=0.165


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 TT=0.822664 delT=0.177336
gnomAD - Genomes Global Study-wide 138942 TT=0.818154 delT=0.181846
gnomAD - Genomes European Sub 75322 TT=0.78794 delT=0.21206
gnomAD - Genomes African Sub 41524 TT=0.87345 delT=0.12655
gnomAD - Genomes American Sub 13520 TT=0.82241 delT=0.17759
gnomAD - Genomes Ashkenazi Jewish Sub 3322 TT=0.8089 delT=0.1911
gnomAD - Genomes East Asian Sub 3120 TT=0.7949 delT=0.2051
gnomAD - Genomes Other Sub 2134 TT=0.8304 delT=0.1696
Allele Frequency Aggregator Total Global 18520 TT=0.81274 delT=0.18726
Allele Frequency Aggregator European Sub 14152 TT=0.79593 delT=0.20407
Allele Frequency Aggregator African Sub 2898 TT=0.8816 delT=0.1184
Allele Frequency Aggregator Latin American 2 Sub 610 TT=0.851 delT=0.149
Allele Frequency Aggregator Other Sub 504 TT=0.835 delT=0.165
Allele Frequency Aggregator Latin American 1 Sub 146 TT=0.822 delT=0.178
Allele Frequency Aggregator Asian Sub 112 TT=0.795 delT=0.205
Allele Frequency Aggregator South Asian Sub 98 TT=0.86 delT=0.14
1000Genomes_30x Global Study-wide 6404 TT=0.8385 delT=0.1615
1000Genomes_30x African Sub 1786 TT=0.8875 delT=0.1125
1000Genomes_30x Europe Sub 1266 TT=0.7559 delT=0.2441
1000Genomes_30x South Asian Sub 1202 TT=0.8785 delT=0.1215
1000Genomes_30x East Asian Sub 1170 TT=0.7940 delT=0.2060
1000Genomes_30x American Sub 980 TT=0.860 delT=0.140
1000Genomes Global Study-wide 5008 TT=0.8375 delT=0.1625
1000Genomes African Sub 1322 TT=0.8835 delT=0.1165
1000Genomes East Asian Sub 1008 TT=0.8006 delT=0.1994
1000Genomes Europe Sub 1006 TT=0.7634 delT=0.2366
1000Genomes South Asian Sub 978 TT=0.873 delT=0.127
1000Genomes American Sub 694 TT=0.860 delT=0.140
Genetic variation in the Estonian population Estonian Study-wide 4480 TT=0.7987 delT=0.2013
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 TT=0.7846 delT=0.2154
UK 10K study - Twins TWIN COHORT Study-wide 3708 TT=0.7783 delT=0.2217
Genome of the Netherlands Release 5 Genome of the Netherlands Study-wide 998 TT=0.775 delT=0.225
Northern Sweden ACPOP Study-wide 600 TT=0.815 delT=0.185
The Danish reference pan genome Danish Study-wide 40 TT=0.62 delT=0.38
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 4 NC_000004.12:g.42600984del
GRCh38.p14 chr 4 NC_000004.12:g.42600984dup
GRCh37.p13 chr 4 NC_000004.11:g.42603001del
GRCh37.p13 chr 4 NC_000004.11:g.42603001dup
Gene: ATP8A1, ATPase phospholipid transporting 8A1 (minus strand)
Molecule type Change Amino acid[Codon] SO Term
ATP8A1 transcript variant 2 NM_001105529.1:c.410-465d…

NM_001105529.1:c.410-465del

N/A Intron Variant
ATP8A1 transcript variant 3 NM_001400024.1:c.410-465d…

NM_001400024.1:c.410-465del

N/A Intron Variant
ATP8A1 transcript variant 4 NM_001400025.1:c.410-465d…

NM_001400025.1:c.410-465del

N/A Intron Variant
ATP8A1 transcript variant 5 NM_001400026.1:c.410-465d…

NM_001400026.1:c.410-465del

N/A Intron Variant
ATP8A1 transcript variant 6 NM_001400027.1:c.-9-465del N/A Intron Variant
ATP8A1 transcript variant 1 NM_006095.2:c.410-465del N/A Intron Variant
ATP8A1 transcript variant X1 XM_011513615.2:c.410-465d…

XM_011513615.2:c.410-465del

N/A Intron Variant
ATP8A1 transcript variant X2 XM_011513616.3:c.410-465d…

XM_011513616.3:c.410-465del

N/A Intron Variant
ATP8A1 transcript variant X3 XM_047449508.1:c.410-465d…

XM_047449508.1:c.410-465del

N/A Intron Variant
ATP8A1 transcript variant X4 XM_047449509.1:c.-9-465del N/A Intron Variant
ATP8A1 transcript variant X5 XM_047449510.1:c.410-465d…

XM_047449510.1:c.410-465del

N/A Intron Variant
ATP8A1 transcript variant X6 XM_047449511.1:c.410-465d…

XM_047449511.1:c.410-465del

N/A Intron 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 TT= delT dupT
GRCh38.p14 chr 4 NC_000004.12:g.42600983_42600984= NC_000004.12:g.42600984del NC_000004.12:g.42600984dup
GRCh37.p13 chr 4 NC_000004.11:g.42603000_42603001= NC_000004.11:g.42603001del NC_000004.11:g.42603001dup
ATP8A1 transcript variant 2 NM_001105529.1:c.410-465= NM_001105529.1:c.410-465del NM_001105529.1:c.410-465dup
ATP8A1 transcript variant 3 NM_001400024.1:c.410-465= NM_001400024.1:c.410-465del NM_001400024.1:c.410-465dup
ATP8A1 transcript variant 4 NM_001400025.1:c.410-465= NM_001400025.1:c.410-465del NM_001400025.1:c.410-465dup
ATP8A1 transcript variant 5 NM_001400026.1:c.410-465= NM_001400026.1:c.410-465del NM_001400026.1:c.410-465dup
ATP8A1 transcript variant 6 NM_001400027.1:c.-9-465= NM_001400027.1:c.-9-465del NM_001400027.1:c.-9-465dup
ATP8A1 transcript variant 1 NM_006095.2:c.410-465= NM_006095.2:c.410-465del NM_006095.2:c.410-465dup
ATP8A1 transcript variant X1 XM_005248043.1:c.410-465= XM_005248043.1:c.410-465del XM_005248043.1:c.410-465dup
ATP8A1 transcript variant X1 XM_011513615.2:c.410-465= XM_011513615.2:c.410-465del XM_011513615.2:c.410-465dup
ATP8A1 transcript variant X2 XM_011513616.3:c.410-465= XM_011513616.3:c.410-465del XM_011513616.3:c.410-465dup
ATP8A1 transcript variant X3 XM_047449508.1:c.410-465= XM_047449508.1:c.410-465del XM_047449508.1:c.410-465dup
ATP8A1 transcript variant X4 XM_047449509.1:c.-9-465= XM_047449509.1:c.-9-465del XM_047449509.1:c.-9-465dup
ATP8A1 transcript variant X5 XM_047449510.1:c.410-465= XM_047449510.1:c.410-465del XM_047449510.1:c.410-465dup
ATP8A1 transcript variant X6 XM_047449511.1:c.410-465= XM_047449511.1:c.410-465del XM_047449511.1:c.410-465dup
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#.

53 SubSNP, 15 Frequency submissions
No Submitter Submission ID Date (Build)
1 HGSV ss83302885 Sep 08, 2015 (146)
2 GMI ss287746374 May 09, 2011 (137)
3 GMI ss288513466 May 04, 2012 (137)
4 PJP ss295162408 May 09, 2011 (137)
5 1000GENOMES ss326511614 May 09, 2011 (137)
6 1000GENOMES ss326542100 May 09, 2011 (137)
7 1000GENOMES ss326702398 May 09, 2011 (137)
8 1000GENOMES ss500147737 May 04, 2012 (137)
9 LUNTER ss551355429 Apr 25, 2013 (138)
10 LUNTER ss551471005 Apr 25, 2013 (138)
11 LUNTER ss553119271 Apr 25, 2013 (138)
12 TISHKOFF ss554081425 Apr 25, 2013 (138)
13 TISHKOFF ss554081427 Apr 25, 2013 (138)
14 SSMP ss663510183 Apr 01, 2015 (144)
15 EVA-GONL ss980025796 Aug 21, 2014 (142)
16 1000GENOMES ss1372086940 Aug 21, 2014 (142)
17 DDI ss1536404413 Apr 01, 2015 (144)
18 EVA_GENOME_DK ss1576217690 Apr 01, 2015 (144)
19 EVA_DECODE ss1589521167 Apr 01, 2015 (144)
20 EVA_UK10K_ALSPAC ss1704133203 Apr 01, 2015 (144)
21 EVA_UK10K_TWINSUK ss1704133801 Apr 01, 2015 (144)
22 HAMMER_LAB ss1801339567 Sep 08, 2015 (146)
23 JJLAB ss2030593630 Sep 14, 2016 (149)
24 SYSTEMSBIOZJU ss2625607411 Nov 08, 2017 (151)
25 GNOMAD ss2808293464 Nov 08, 2017 (151)
26 SWEGEN ss2994528269 Nov 08, 2017 (151)
27 MCHAISSO ss3064098196 Nov 08, 2017 (151)
28 MCHAISSO ss3065945317 Nov 08, 2017 (151)
29 BEROUKHIMLAB ss3644152577 Oct 12, 2018 (152)
30 BIOINF_KMB_FNS_UNIBA ss3645790012 Oct 12, 2018 (152)
31 URBANLAB ss3647707442 Oct 12, 2018 (152)
32 EGCUT_WGS ss3662449086 Jul 13, 2019 (153)
33 EVA_DECODE ss3711886807 Jul 13, 2019 (153)
34 ACPOP ss3731076002 Jul 13, 2019 (153)
35 KHV_HUMAN_GENOMES ss3804832222 Jul 13, 2019 (153)
36 EVA ss3828498253 Apr 26, 2020 (154)
37 EVA ss3837685156 Apr 26, 2020 (154)
38 EVA ss3843120345 Apr 26, 2020 (154)
39 TOPMED ss4610914464 Apr 26, 2021 (155)
40 TOMMO_GENOMICS ss5165265101 Apr 26, 2021 (155)
41 TOMMO_GENOMICS ss5165265102 Apr 26, 2021 (155)
42 1000G_HIGH_COVERAGE ss5258886150 Oct 13, 2022 (156)
43 HUGCELL_USP ss5457704585 Oct 13, 2022 (156)
44 EVA ss5507480035 Oct 13, 2022 (156)
45 1000G_HIGH_COVERAGE ss5539763017 Oct 13, 2022 (156)
46 SANFORD_IMAGENETICS ss5634839771 Oct 13, 2022 (156)
47 TOMMO_GENOMICS ss5699208357 Oct 13, 2022 (156)
48 TOMMO_GENOMICS ss5699208358 Oct 13, 2022 (156)
49 YY_MCH ss5804976498 Oct 13, 2022 (156)
50 EVA ss5843879482 Oct 13, 2022 (156)
51 EVA ss5854187891 Oct 13, 2022 (156)
52 EVA ss5863111555 Oct 13, 2022 (156)
53 EVA ss5963233368 Oct 13, 2022 (156)
54 1000Genomes NC_000004.11 - 42603000 Oct 12, 2018 (152)
55 1000Genomes_30x NC_000004.12 - 42600983 Oct 13, 2022 (156)
56 The Avon Longitudinal Study of Parents and Children NC_000004.11 - 42603000 Oct 12, 2018 (152)
57 Genetic variation in the Estonian population NC_000004.11 - 42603000 Oct 12, 2018 (152)
58 The Danish reference pan genome NC_000004.11 - 42603000 Apr 26, 2020 (154)
59 gnomAD - Genomes NC_000004.12 - 42600983 Apr 26, 2021 (155)
60 Genome of the Netherlands Release 5 NC_000004.11 - 42603000 Apr 26, 2020 (154)
61 Northern Sweden NC_000004.11 - 42603000 Jul 13, 2019 (153)
62 8.3KJPN

Submission ignored due to conflicting rows:
Row 23234408 (NC_000004.11:42602999:T: 4588/16760)
Row 23234409 (NC_000004.11:42602999::T 1/16760)

- Apr 26, 2021 (155)
63 8.3KJPN

Submission ignored due to conflicting rows:
Row 23234408 (NC_000004.11:42602999:T: 4588/16760)
Row 23234409 (NC_000004.11:42602999::T 1/16760)

- Apr 26, 2021 (155)
64 14KJPN

Submission ignored due to conflicting rows:
Row 33045461 (NC_000004.12:42600982:T: 7662/28258)
Row 33045462 (NC_000004.12:42600982::T 1/28258)

- Oct 13, 2022 (156)
65 14KJPN

Submission ignored due to conflicting rows:
Row 33045461 (NC_000004.12:42600982:T: 7662/28258)
Row 33045462 (NC_000004.12:42600982::T 1/28258)

- Oct 13, 2022 (156)
66 TopMed NC_000004.12 - 42600983 Apr 26, 2021 (155)
67 UK 10K study - Twins NC_000004.11 - 42603000 Oct 12, 2018 (152)
68 ALFA NC_000004.12 - 42600983 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)
rs141694453 May 11, 2012 (137)
rs143792321 May 04, 2012 (137)
rs368793440 May 15, 2013 (138)
rs373326211 May 13, 2013 (138)
Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
ss83302885 NC_000004.9:42443928:T: NC_000004.12:42600982:TT:T (self)
ss288513466, ss295162408, ss326511614, ss326542100, ss326702398, ss551355429, ss551471005, ss553119271, ss1589521167 NC_000004.10:42297756:T: NC_000004.12:42600982:TT:T (self)
20773292, 11575390, 8187334, 905698, 5100537, 4360867, 11575390, ss500147737, ss554081425, ss663510183, ss980025796, ss1372086940, ss1536404413, ss1576217690, ss1704133203, ss1704133801, ss1801339567, ss2030593630, ss2625607411, ss2808293464, ss2994528269, ss3644152577, ss3662449086, ss3731076002, ss3828498253, ss3837685156, ss5165265101, ss5634839771, ss5843879482, ss5963233368 NC_000004.11:42602999:T: NC_000004.12:42600982:TT:T (self)
ss554081427 NC_000004.11:42603000:T: NC_000004.12:42600982:TT:T (self)
27288952, 147068019, 448292020, ss3064098196, ss3065945317, ss3645790012, ss3647707442, ss3711886807, ss3804832222, ss3843120345, ss4610914464, ss5258886150, ss5457704585, ss5539763017, ss5699208357, ss5804976498, ss5854187891, ss5863111555 NC_000004.12:42600982:T: NC_000004.12:42600982:TT:T (self)
11002273784 NC_000004.12:42600982:TT:T NC_000004.12:42600982:TT:T (self)
ss287746374 NT_006238.11:2305903:T: NC_000004.12:42600982:TT:T (self)
ss5165265102, ss5507480035 NC_000004.11:42602999::T NC_000004.12:42600982:TT:TTT (self)
ss5699208358 NC_000004.12:42600982::T NC_000004.12:42600982:TT:TTT
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 rs59622418

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