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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.

rs572880

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr1:232457115 (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
Variation Type
SNV Single Nucleotide Variation
Frequency
C=0.286535 (75843/264690, TOPMED)
C=0.293757 (41143/140058, GnomAD)
C=0.33048 (10200/30864, ALFA) (+ 17 more)
C=0.21195 (5989/28256, 14KJPN)
C=0.20895 (3502/16760, 8.3KJPN)
C=0.2744 (1757/6404, 1000G_30x)
C=0.2764 (1384/5008, 1000G)
C=0.3232 (1448/4480, Estonian)
C=0.3287 (1267/3854, ALSPAC)
C=0.3358 (1245/3708, TWINSUK)
C=0.2341 (686/2930, KOREAN)
C=0.2238 (410/1832, Korea1K)
C=0.315 (314/998, GoNL)
C=0.283 (170/600, NorthernSweden)
T=0.352 (105/298, SGDP_PRJ)
C=0.449 (97/216, Qatari)
C=0.313 (67/214, Vietnamese)
C=0.30 (12/40, GENOME_DK)
T=0.50 (17/34, Siberian)
C=0.50 (17/34, Siberian)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
SIPA1L2 : 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 30864 T=0.66952 C=0.33048
European Sub 24734 T=0.65036 C=0.34964
African Sub 3168 T=0.7973 C=0.2027
African Others Sub 124 T=0.758 C=0.242
African American Sub 3044 T=0.7989 C=0.2011
Asian Sub 128 T=0.711 C=0.289
East Asian Sub 100 T=0.72 C=0.28
Other Asian Sub 28 T=0.68 C=0.32
Latin American 1 Sub 168 T=0.673 C=0.327
Latin American 2 Sub 700 T=0.799 C=0.201
South Asian Sub 114 T=0.658 C=0.342
Other Sub 1852 T=0.6555 C=0.3445


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 T=0.713465 C=0.286535
gnomAD - Genomes Global Study-wide 140058 T=0.706243 C=0.293757
gnomAD - Genomes European Sub 75844 T=0.65925 C=0.34075
gnomAD - Genomes African Sub 41972 T=0.78328 C=0.21672
gnomAD - Genomes American Sub 13648 T=0.75528 C=0.24472
gnomAD - Genomes Ashkenazi Jewish Sub 3322 T=0.5518 C=0.4482
gnomAD - Genomes East Asian Sub 3124 T=0.7545 C=0.2455
gnomAD - Genomes Other Sub 2148 T=0.7174 C=0.2826
Allele Frequency Aggregator Total Global 30864 T=0.66952 C=0.33048
Allele Frequency Aggregator European Sub 24734 T=0.65036 C=0.34964
Allele Frequency Aggregator African Sub 3168 T=0.7973 C=0.2027
Allele Frequency Aggregator Other Sub 1852 T=0.6555 C=0.3445
Allele Frequency Aggregator Latin American 2 Sub 700 T=0.799 C=0.201
Allele Frequency Aggregator Latin American 1 Sub 168 T=0.673 C=0.327
Allele Frequency Aggregator Asian Sub 128 T=0.711 C=0.289
Allele Frequency Aggregator South Asian Sub 114 T=0.658 C=0.342
14KJPN JAPANESE Study-wide 28256 T=0.78805 C=0.21195
8.3KJPN JAPANESE Study-wide 16760 T=0.79105 C=0.20895
1000Genomes_30x Global Study-wide 6404 T=0.7256 C=0.2744
1000Genomes_30x African Sub 1786 T=0.7850 C=0.2150
1000Genomes_30x Europe Sub 1266 T=0.6319 C=0.3681
1000Genomes_30x South Asian Sub 1202 T=0.6730 C=0.3270
1000Genomes_30x East Asian Sub 1170 T=0.7231 C=0.2769
1000Genomes_30x American Sub 980 T=0.806 C=0.194
1000Genomes Global Study-wide 5008 T=0.7236 C=0.2764
1000Genomes African Sub 1322 T=0.7874 C=0.2126
1000Genomes East Asian Sub 1008 T=0.7292 C=0.2708
1000Genomes Europe Sub 1006 T=0.6322 C=0.3678
1000Genomes South Asian Sub 978 T=0.668 C=0.332
1000Genomes American Sub 694 T=0.805 C=0.195
Genetic variation in the Estonian population Estonian Study-wide 4480 T=0.6768 C=0.3232
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 T=0.6713 C=0.3287
UK 10K study - Twins TWIN COHORT Study-wide 3708 T=0.6642 C=0.3358
KOREAN population from KRGDB KOREAN Study-wide 2930 T=0.7659 C=0.2341
Korean Genome Project KOREAN Study-wide 1832 T=0.7762 C=0.2238
Genome of the Netherlands Release 5 Genome of the Netherlands Study-wide 998 T=0.685 C=0.315
Northern Sweden ACPOP Study-wide 600 T=0.717 C=0.283
SGDP_PRJ Global Study-wide 298 T=0.352 C=0.648
Qatari Global Study-wide 216 T=0.551 C=0.449
A Vietnamese Genetic Variation Database Global Study-wide 214 T=0.687 C=0.313
The Danish reference pan genome Danish Study-wide 40 T=0.70 C=0.30
Siberian Global Study-wide 34 T=0.50 C=0.50
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 1 NC_000001.11:g.232457115T>C
GRCh37.p13 chr 1 NC_000001.10:g.232592861T>C
Gene: SIPA1L2, signal induced proliferation associated 1 like 2 (minus strand)
Molecule type Change Amino acid[Codon] SO Term
SIPA1L2 transcript variant 2 NM_001377488.1:c.3095+377…

NM_001377488.1:c.3095+3772A>G

N/A Intron Variant
SIPA1L2 transcript variant 1 NM_020808.5:c.3095+3772A>G N/A Intron Variant
SIPA1L2 transcript variant X8 XM_005273213.5:c.3095+377…

XM_005273213.5:c.3095+3772A>G

N/A Intron Variant
SIPA1L2 transcript variant X5 XM_017001896.2:c.3095+377…

XM_017001896.2:c.3095+3772A>G

N/A Intron Variant
SIPA1L2 transcript variant X1 XM_047426139.1:c.3095+377…

XM_047426139.1:c.3095+3772A>G

N/A Intron Variant
SIPA1L2 transcript variant X2 XM_047426140.1:c.3095+377…

XM_047426140.1:c.3095+3772A>G

N/A Intron Variant
SIPA1L2 transcript variant X3 XM_047426141.1:c.3095+377…

XM_047426141.1:c.3095+3772A>G

N/A Intron Variant
SIPA1L2 transcript variant X4 XM_047426142.1:c.3095+377…

XM_047426142.1:c.3095+3772A>G

N/A Intron Variant
SIPA1L2 transcript variant X6 XM_047426143.1:c.3095+377…

XM_047426143.1:c.3095+3772A>G

N/A Intron Variant
SIPA1L2 transcript variant X7 XM_047426144.1:c.3095+377…

XM_047426144.1:c.3095+3772A>G

N/A Intron Variant
SIPA1L2 transcript variant X9 XM_047426145.1:c.3095+377…

XM_047426145.1:c.3095+3772A>G

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 T= C
GRCh38.p14 chr 1 NC_000001.11:g.232457115= NC_000001.11:g.232457115T>C
GRCh37.p13 chr 1 NC_000001.10:g.232592861= NC_000001.10:g.232592861T>C
SIPA1L2 transcript variant 2 NM_001377488.1:c.3095+3772= NM_001377488.1:c.3095+3772A>G
SIPA1L2 transcript NM_020808.3:c.3095+3772= NM_020808.3:c.3095+3772A>G
SIPA1L2 transcript variant 1 NM_020808.5:c.3095+3772= NM_020808.5:c.3095+3772A>G
SIPA1L2 transcript variant X1 XM_005273209.1:c.3095+3772= XM_005273209.1:c.3095+3772A>G
SIPA1L2 transcript variant X2 XM_005273210.1:c.3095+3772= XM_005273210.1:c.3095+3772A>G
SIPA1L2 transcript variant X4 XM_005273211.1:c.3095+3772= XM_005273211.1:c.3095+3772A>G
SIPA1L2 transcript variant X4 XM_005273212.1:c.3095+3772= XM_005273212.1:c.3095+3772A>G
SIPA1L2 transcript variant X5 XM_005273213.1:c.3095+3772= XM_005273213.1:c.3095+3772A>G
SIPA1L2 transcript variant X8 XM_005273213.5:c.3095+3772= XM_005273213.5:c.3095+3772A>G
SIPA1L2 transcript variant X8 XM_005273214.1:c.3095+3772= XM_005273214.1:c.3095+3772A>G
SIPA1L2 transcript variant X7 XM_005273215.1:c.3095+3772= XM_005273215.1:c.3095+3772A>G
SIPA1L2 transcript variant X8 XM_005273216.1:c.317+3772= XM_005273216.1:c.317+3772A>G
SIPA1L2 transcript variant X5 XM_017001896.2:c.3095+3772= XM_017001896.2:c.3095+3772A>G
SIPA1L2 transcript variant X1 XM_047426139.1:c.3095+3772= XM_047426139.1:c.3095+3772A>G
SIPA1L2 transcript variant X2 XM_047426140.1:c.3095+3772= XM_047426140.1:c.3095+3772A>G
SIPA1L2 transcript variant X3 XM_047426141.1:c.3095+3772= XM_047426141.1:c.3095+3772A>G
SIPA1L2 transcript variant X4 XM_047426142.1:c.3095+3772= XM_047426142.1:c.3095+3772A>G
SIPA1L2 transcript variant X6 XM_047426143.1:c.3095+3772= XM_047426143.1:c.3095+3772A>G
SIPA1L2 transcript variant X7 XM_047426144.1:c.3095+3772= XM_047426144.1:c.3095+3772A>G
SIPA1L2 transcript variant X9 XM_047426145.1:c.3095+3772= XM_047426145.1:c.3095+3772A>G
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#.

77 SubSNP, 19 Frequency submissions
No Submitter Submission ID Date (Build)
1 SC_JCM ss744240 Aug 11, 2000 (83)
2 TSC-CSHL ss1464052 Oct 13, 2000 (123)
3 SC_JCM ss2623715 Nov 09, 2000 (92)
4 SC_JCM ss3486693 Sep 28, 2001 (100)
5 SC_JCM ss3908385 Sep 28, 2001 (100)
6 TSC-CSHL ss5495717 Oct 08, 2002 (108)
7 SC_SNP ss12994122 Dec 05, 2003 (119)
8 CSHL-HAPMAP ss19868874 Feb 27, 2004 (120)
9 ABI ss28532892 Dec 02, 2004 (126)
10 1000GENOMES ss109031266 Jan 23, 2009 (130)
11 ENSEMBL ss161228711 Dec 01, 2009 (131)
12 COMPLETE_GENOMICS ss167562679 Jul 04, 2010 (132)
13 1000GENOMES ss210764823 Jul 14, 2010 (132)
14 1000GENOMES ss218940835 Jul 14, 2010 (132)
15 1000GENOMES ss230946110 Jul 14, 2010 (132)
16 1000GENOMES ss238551883 Jul 15, 2010 (132)
17 GMI ss276261310 May 04, 2012 (137)
18 PJP ss290755928 May 09, 2011 (134)
19 ILLUMINA ss482261036 May 04, 2012 (137)
20 ILLUMINA ss484282998 May 04, 2012 (137)
21 ILLUMINA ss536467268 Sep 08, 2015 (146)
22 TISHKOFF ss555208718 Apr 25, 2013 (138)
23 SSMP ss648781844 Apr 25, 2013 (138)
24 ILLUMINA ss780595453 Aug 21, 2014 (142)
25 ILLUMINA ss782587559 Aug 21, 2014 (142)
26 ILLUMINA ss836088453 Aug 21, 2014 (142)
27 EVA-GONL ss976259989 Aug 21, 2014 (142)
28 JMKIDD_LAB ss1068688706 Aug 21, 2014 (142)
29 1000GENOMES ss1295085153 Aug 21, 2014 (142)
30 DDI ss1426144624 Apr 01, 2015 (144)
31 EVA_GENOME_DK ss1574752020 Apr 01, 2015 (144)
32 EVA_DECODE ss1585659875 Apr 01, 2015 (144)
33 EVA_UK10K_ALSPAC ss1602371628 Apr 01, 2015 (144)
34 EVA_UK10K_TWINSUK ss1645365661 Apr 01, 2015 (144)
35 WEILL_CORNELL_DGM ss1919481264 Feb 12, 2016 (147)
36 GENOMED ss1967000004 Jul 19, 2016 (147)
37 JJLAB ss2020265934 Sep 14, 2016 (149)
38 USC_VALOUEV ss2148301941 Dec 20, 2016 (150)
39 HUMAN_LONGEVITY ss2170982865 Dec 20, 2016 (150)
40 SYSTEMSBIOZJU ss2624645355 Nov 08, 2017 (151)
41 ILLUMINA ss2632643582 Nov 08, 2017 (151)
42 GRF ss2698302878 Nov 08, 2017 (151)
43 GNOMAD ss2767449277 Nov 08, 2017 (151)
44 SWEGEN ss2988629632 Nov 08, 2017 (151)
45 BIOINF_KMB_FNS_UNIBA ss3023893851 Nov 08, 2017 (151)
46 CSHL ss3343962833 Nov 08, 2017 (151)
47 ILLUMINA ss3626334043 Oct 11, 2018 (152)
48 ILLUMINA ss3630672693 Oct 11, 2018 (152)
49 ILLUMINA ss3641646310 Oct 11, 2018 (152)
50 EGCUT_WGS ss3656588511 Jul 12, 2019 (153)
51 EVA_DECODE ss3688843802 Jul 12, 2019 (153)
52 ACPOP ss3727957082 Jul 12, 2019 (153)
53 EVA ss3747473456 Jul 12, 2019 (153)
54 PACBIO ss3783716852 Jul 12, 2019 (153)
55 PACBIO ss3789324242 Jul 12, 2019 (153)
56 PACBIO ss3794196659 Jul 12, 2019 (153)
57 KHV_HUMAN_GENOMES ss3800475217 Jul 12, 2019 (153)
58 EVA ss3826700626 Apr 25, 2020 (154)
59 EVA ss3836752106 Apr 25, 2020 (154)
60 EVA ss3842164612 Apr 25, 2020 (154)
61 SGDP_PRJ ss3851124584 Apr 25, 2020 (154)
62 KRGDB ss3896473574 Apr 25, 2020 (154)
63 KOGIC ss3946719188 Apr 25, 2020 (154)
64 TOPMED ss4487383571 Apr 25, 2021 (155)
65 TOMMO_GENOMICS ss5148931441 Apr 25, 2021 (155)
66 1000G_HIGH_COVERAGE ss5246175528 Oct 12, 2022 (156)
67 EVA ss5314691129 Oct 12, 2022 (156)
68 EVA ss5325484824 Oct 12, 2022 (156)
69 HUGCELL_USP ss5446573339 Oct 12, 2022 (156)
70 1000G_HIGH_COVERAGE ss5520463543 Oct 12, 2022 (156)
71 SANFORD_IMAGENETICS ss5627662849 Oct 12, 2022 (156)
72 TOMMO_GENOMICS ss5676836639 Oct 12, 2022 (156)
73 YY_MCH ss5801736326 Oct 12, 2022 (156)
74 EVA ss5833416224 Oct 12, 2022 (156)
75 EVA ss5849334051 Oct 12, 2022 (156)
76 EVA ss5912411421 Oct 12, 2022 (156)
77 EVA ss5939511391 Oct 12, 2022 (156)
78 1000Genomes NC_000001.10 - 232592861 Oct 11, 2018 (152)
79 1000Genomes_30x NC_000001.11 - 232457115 Oct 12, 2022 (156)
80 The Avon Longitudinal Study of Parents and Children NC_000001.10 - 232592861 Oct 11, 2018 (152)
81 Genetic variation in the Estonian population NC_000001.10 - 232592861 Oct 11, 2018 (152)
82 The Danish reference pan genome NC_000001.10 - 232592861 Apr 25, 2020 (154)
83 gnomAD - Genomes NC_000001.11 - 232457115 Apr 25, 2021 (155)
84 Genome of the Netherlands Release 5 NC_000001.10 - 232592861 Apr 25, 2020 (154)
85 KOREAN population from KRGDB NC_000001.10 - 232592861 Apr 25, 2020 (154)
86 Korean Genome Project NC_000001.11 - 232457115 Apr 25, 2020 (154)
87 Northern Sweden NC_000001.10 - 232592861 Jul 12, 2019 (153)
88 Qatari NC_000001.10 - 232592861 Apr 25, 2020 (154)
89 SGDP_PRJ NC_000001.10 - 232592861 Apr 25, 2020 (154)
90 Siberian NC_000001.10 - 232592861 Apr 25, 2020 (154)
91 8.3KJPN NC_000001.10 - 232592861 Apr 25, 2021 (155)
92 14KJPN NC_000001.11 - 232457115 Oct 12, 2022 (156)
93 TopMed NC_000001.11 - 232457115 Apr 25, 2021 (155)
94 UK 10K study - Twins NC_000001.10 - 232592861 Oct 11, 2018 (152)
95 A Vietnamese Genetic Variation Database NC_000001.10 - 232592861 Jul 12, 2019 (153)
96 ALFA NC_000001.11 - 232457115 Apr 25, 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)
rs1124133 Sep 24, 2004 (123)
rs1766575 Jan 18, 2001 (92)
rs17878873 Mar 10, 2006 (126)
Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
ss109031266, ss167562679, ss210764823, ss276261310, ss290755928, ss482261036, ss1585659875 NC_000001.9:230659483:T:C NC_000001.11:232457114:T:C (self)
5955436, 3293570, 2326759, 1930658, 1440000, 3650968, 1241947, 1523194, 3141564, 818295, 6900748, 3293570, 716514, ss218940835, ss230946110, ss238551883, ss484282998, ss536467268, ss555208718, ss648781844, ss780595453, ss782587559, ss836088453, ss976259989, ss1068688706, ss1295085153, ss1426144624, ss1574752020, ss1602371628, ss1645365661, ss1919481264, ss1967000004, ss2020265934, ss2148301941, ss2624645355, ss2632643582, ss2698302878, ss2767449277, ss2988629632, ss3343962833, ss3626334043, ss3630672693, ss3641646310, ss3656588511, ss3727957082, ss3747473456, ss3783716852, ss3789324242, ss3794196659, ss3826700626, ss3836752106, ss3851124584, ss3896473574, ss5148931441, ss5314691129, ss5325484824, ss5627662849, ss5833416224, ss5939511391 NC_000001.10:232592860:T:C NC_000001.11:232457114:T:C (self)
7989478, 42711491, 3097189, 10673743, 50989906, 3354333824, ss2170982865, ss3023893851, ss3688843802, ss3800475217, ss3842164612, ss3946719188, ss4487383571, ss5246175528, ss5446573339, ss5520463543, ss5676836639, ss5801736326, ss5849334051, ss5912411421 NC_000001.11:232457114:T:C NC_000001.11:232457114:T:C (self)
ss12994122 NT_004433.15:231315:T:C NC_000001.11:232457114:T:C (self)
ss19868874 NT_004433.16:268209:T:C NC_000001.11:232457114:T:C (self)
ss744240, ss1464052, ss2623715, ss3486693, ss3908385, ss5495717, ss28532892, ss161228711 NT_167186.1:26110639:T:C NC_000001.11:232457114:T:C (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 rs572880

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