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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.

rs715494

Current Build 155

Released April 9, 2021

Organism
Homo sapiens
Position
chr22:29386444 (GRCh38.p13) 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
A>C
Variation Type
SNV Single Nucleotide Variation
Frequency
A=0.369614 (97833/264690, TOPMED)
A=0.364097 (50970/139990, GnomAD)
A=0.40414 (11699/28948, ALFA) (+ 15 more)
A=0.26468 (4436/16760, 8.3KJPN)
A=0.3303 (1654/5008, 1000G)
A=0.4145 (1857/4480, Estonian)
A=0.4504 (1736/3854, ALSPAC)
A=0.4353 (1614/3708, TWINSUK)
A=0.2896 (545/1882, HapMap)
A=0.2882 (528/1832, Korea1K)
A=0.438 (437/998, GoNL)
A=0.415 (249/600, NorthernSweden)
A=0.214 (99/462, SGDP_PRJ)
A=0.468 (101/216, Qatari)
A=0.299 (64/214, Vietnamese)
A=0.33 (16/48, Siberian)
A=0.40 (16/40, GENOME_DK)
A=0.1 (1/8, KOREAN)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
AP1B1 : Intron Variant
RFPL1 : 2KB Upstream Variant
Publications
0 citations
Genomic View
See rs on genome
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.p13 chr 22 NC_000022.11:g.29386444A>C
GRCh37.p13 chr 22 NC_000022.10:g.29782433A>C
Gene: AP1B1, adaptor related protein complex 1 subunit beta 1 (minus strand)
Molecule type Change Amino acid[Codon] SO Term
AP1B1 transcript variant 1 NM_001127.4:c.-28+1980T>G N/A Intron Variant
AP1B1 transcript variant 3 NM_001166019.2:c.-28+1980…

NM_001166019.2:c.-28+1980T>G

N/A Intron Variant
AP1B1 transcript variant 4 NM_001378562.1:c.-28+1980…

NM_001378562.1:c.-28+1980T>G

N/A Intron Variant
AP1B1 transcript variant 5 NM_001378563.1:c.-28+1980…

NM_001378563.1:c.-28+1980T>G

N/A Intron Variant
AP1B1 transcript variant 6 NM_001378564.1:c.-93+1980…

NM_001378564.1:c.-93+1980T>G

N/A Intron Variant
AP1B1 transcript variant 7 NM_001378565.1:c.-93+1980…

NM_001378565.1:c.-93+1980T>G

N/A Intron Variant
AP1B1 transcript variant 8 NM_001378566.1:c.-28+1980…

NM_001378566.1:c.-28+1980T>G

N/A Intron Variant
AP1B1 transcript variant 2 NM_145730.3:c.-28+1980T>G N/A Intron Variant
Gene: RFPL1, ret finger protein like 1 (plus strand) : 2KB Upstream Variant
Molecule type Change Amino acid[Codon] SO Term
RFPL1 transcript variant 2 NM_001393612.1:c. N/A Upstream Transcript Variant
RFPL1 transcript variant 1 NM_021026.2:c. N/A N/A
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

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: 20201027095038
Population Group Sample Size Ref Allele Alt Allele
Total Global 28948 A=0.40414 C=0.59586
European Sub 19066 A=0.44467 C=0.55533
African Sub 4792 A=0.1667 C=0.8333
African Others Sub 160 A=0.119 C=0.881
African American Sub 4632 A=0.1684 C=0.8316
Asian Sub 172 A=0.285 C=0.715
East Asian Sub 112 A=0.304 C=0.696
Other Asian Sub 60 A=0.25 C=0.75
Latin American 1 Sub 314 A=0.433 C=0.567
Latin American 2 Sub 2828 A=0.5064 C=0.4936
South Asian Sub 110 A=0.445 C=0.555
Other Sub 1666 A=0.4538 C=0.5462


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=0.369614 C=0.630386
gnomAD - Genomes Global Study-wide 139990 A=0.364097 C=0.635903
gnomAD - Genomes European Sub 75818 A=0.43806 C=0.56194
gnomAD - Genomes African Sub 41956 A=0.16803 C=0.83197
gnomAD - Genomes American Sub 13626 A=0.51813 C=0.48187
gnomAD - Genomes Ashkenazi Jewish Sub 3322 A=0.5578 C=0.4422
gnomAD - Genomes East Asian Sub 3120 A=0.3000 C=0.7000
gnomAD - Genomes Other Sub 2148 A=0.3994 C=0.6006
8.3KJPN JAPANESE Study-wide 16760 A=0.26468 C=0.73532
1000Genomes Global Study-wide 5008 A=0.3303 C=0.6697
1000Genomes African Sub 1322 A=0.1218 C=0.8782
1000Genomes East Asian Sub 1008 A=0.2738 C=0.7262
1000Genomes Europe Sub 1006 A=0.4274 C=0.5726
1000Genomes South Asian Sub 978 A=0.414 C=0.586
1000Genomes American Sub 694 A=0.550 C=0.450
Genetic variation in the Estonian population Estonian Study-wide 4480 A=0.4145 C=0.5855
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 A=0.4504 C=0.5496
UK 10K study - Twins TWIN COHORT Study-wide 3708 A=0.4353 C=0.5647
HapMap Global Study-wide 1882 A=0.2896 C=0.7104
HapMap American Sub 766 A=0.403 C=0.597
HapMap African Sub 688 A=0.119 C=0.881
HapMap Asian Sub 252 A=0.302 C=0.698
HapMap Europe Sub 176 A=0.443 C=0.557
Korean Genome Project KOREAN Study-wide 1832 A=0.2882 C=0.7118
Genome of the Netherlands Release 5 Genome of the Netherlands Study-wide 998 A=0.438 C=0.562
Northern Sweden ACPOP Study-wide 600 A=0.415 C=0.585
SGDP_PRJ Global Study-wide 462 A=0.214 C=0.786
Qatari Global Study-wide 216 A=0.468 C=0.532
A Vietnamese Genetic Variation Database Global Study-wide 214 A=0.299 C=0.701
Siberian Global Study-wide 48 A=0.33 C=0.67
The Danish reference pan genome Danish Study-wide 40 A=0.40 C=0.60
KOREAN population from KRGDB KOREAN Study-wide 8 A=0.1 C=0.9
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= C
GRCh38.p13 chr 22 NC_000022.11:g.29386444= NC_000022.11:g.29386444A>C
GRCh37.p13 chr 22 NC_000022.10:g.29782433= NC_000022.10:g.29782433A>C
AP1B1 transcript variant 1 NM_001127.3:c.-28+1980= NM_001127.3:c.-28+1980T>G
AP1B1 transcript variant 1 NM_001127.4:c.-28+1980= NM_001127.4:c.-28+1980T>G
AP1B1 transcript variant 3 NM_001166019.1:c.-28+1980= NM_001166019.1:c.-28+1980T>G
AP1B1 transcript variant 3 NM_001166019.2:c.-28+1980= NM_001166019.2:c.-28+1980T>G
AP1B1 transcript variant 4 NM_001378562.1:c.-28+1980= NM_001378562.1:c.-28+1980T>G
AP1B1 transcript variant 5 NM_001378563.1:c.-28+1980= NM_001378563.1:c.-28+1980T>G
AP1B1 transcript variant 6 NM_001378564.1:c.-93+1980= NM_001378564.1:c.-93+1980T>G
AP1B1 transcript variant 7 NM_001378565.1:c.-93+1980= NM_001378565.1:c.-93+1980T>G
AP1B1 transcript variant 8 NM_001378566.1:c.-28+1980= NM_001378566.1:c.-28+1980T>G
AP1B1 transcript variant 2 NM_145730.2:c.-28+1980= NM_145730.2:c.-28+1980T>G
AP1B1 transcript variant 2 NM_145730.3:c.-28+1980= NM_145730.3:c.-28+1980T>G
AP1B1 transcript variant X1 XM_005261378.1:c.-28+1980= XM_005261378.1:c.-28+1980T>G
AP1B1 transcript variant X2 XM_005261379.1:c.-28+1980= XM_005261379.1:c.-28+1980T>G
AP1B1 transcript variant X3 XM_005261380.1:c.-28+1980= XM_005261380.1:c.-28+1980T>G
AP1B1 transcript variant X4 XM_005261381.1:c.-28+1980= XM_005261381.1:c.-28+1980T>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#.

84 SubSNP, 18 Frequency submissions
No Submitter Submission ID Date (Build)
1 TSC-CSHL ss27757 Oct 05, 2000 (86)
2 YUSUKE ss3200376 Sep 28, 2001 (100)
3 SC_SNP ss8292243 Apr 21, 2003 (114)
4 SC_SNP ss13390851 Dec 05, 2003 (119)
5 CSHL-HAPMAP ss17719365 Feb 27, 2004 (120)
6 SSAHASNP ss21842233 Apr 05, 2004 (121)
7 PERLEGEN ss24556460 Sep 20, 2004 (123)
8 ABI ss44308099 Mar 15, 2006 (126)
9 ILLUMINA ss65723836 Oct 16, 2006 (127)
10 AFFY ss66136072 Dec 01, 2006 (127)
11 ILLUMINA ss74878372 Dec 07, 2007 (129)
12 AFFY ss76148229 Dec 07, 2007 (129)
13 HGSV ss78636846 Dec 07, 2007 (129)
14 KRIBB_YJKIM ss81434145 Dec 15, 2007 (130)
15 HUMANGENOME_JCVI ss96120933 Feb 06, 2009 (130)
16 BGI ss103852629 Dec 01, 2009 (131)
17 1000GENOMES ss112602595 Jan 25, 2009 (130)
18 1000GENOMES ss114128293 Jan 25, 2009 (130)
19 ILLUMINA-UK ss117386625 Feb 14, 2009 (130)
20 ILLUMINA ss120244563 Dec 01, 2009 (131)
21 ENSEMBL ss144220070 Dec 01, 2009 (131)
22 GMI ss157116820 Dec 01, 2009 (131)
23 COMPLETE_GENOMICS ss167828822 Jul 04, 2010 (132)
24 COMPLETE_GENOMICS ss169084037 Jul 04, 2010 (132)
25 COMPLETE_GENOMICS ss171911862 Jul 04, 2010 (132)
26 AFFY ss172640536 Jul 04, 2010 (132)
27 ILLUMINA ss174265416 Jul 04, 2010 (132)
28 BUSHMAN ss204072250 Jul 04, 2010 (132)
29 BCM-HGSC-SUB ss208828401 Jul 04, 2010 (132)
30 1000GENOMES ss228654080 Jul 14, 2010 (132)
31 1000GENOMES ss238049140 Jul 15, 2010 (132)
32 1000GENOMES ss244172938 Jul 15, 2010 (132)
33 ILLUMINA ss244260799 Jul 04, 2010 (132)
34 BL ss255876181 May 09, 2011 (134)
35 GMI ss283617076 May 04, 2012 (137)
36 PJP ss292750586 May 09, 2011 (134)
37 ILLUMINA ss537442372 Sep 08, 2015 (146)
38 TISHKOFF ss566605124 Apr 25, 2013 (138)
39 SSMP ss662536408 Apr 25, 2013 (138)
40 EVA-GONL ss995297368 Aug 21, 2014 (142)
41 JMKIDD_LAB ss1082620323 Aug 21, 2014 (142)
42 1000GENOMES ss1366965954 Aug 21, 2014 (142)
43 DDI ss1429241810 Apr 01, 2015 (144)
44 EVA_GENOME_DK ss1579731809 Apr 01, 2015 (144)
45 EVA_UK10K_ALSPAC ss1639887829 Apr 01, 2015 (144)
46 EVA_UK10K_TWINSUK ss1682881862 Apr 01, 2015 (144)
47 EVA_DECODE ss1699366467 Apr 01, 2015 (144)
48 EVA_SVP ss1713737060 Apr 01, 2015 (144)
49 HAMMER_LAB ss1809766005 Sep 08, 2015 (146)
50 WEILL_CORNELL_DGM ss1938863618 Feb 12, 2016 (147)
51 GENOMED ss1969262030 Jul 19, 2016 (147)
52 JJLAB ss2030203595 Sep 14, 2016 (149)
53 USC_VALOUEV ss2158819451 Dec 20, 2016 (150)
54 HUMAN_LONGEVITY ss2246926911 Dec 20, 2016 (150)
55 TOPMED ss2413864355 Dec 20, 2016 (150)
56 SYSTEMSBIOZJU ss2629600273 Nov 08, 2017 (151)
57 ILLUMINA ss2633871481 Nov 08, 2017 (151)
58 GRF ss2704570388 Nov 08, 2017 (151)
59 GNOMAD ss2973818469 Nov 08, 2017 (151)
60 SWEGEN ss3019219969 Nov 08, 2017 (151)
61 BIOINF_KMB_FNS_UNIBA ss3028939352 Nov 08, 2017 (151)
62 CSHL ss3352813243 Nov 08, 2017 (151)
63 TOPMED ss3375881405 Nov 08, 2017 (151)
64 ILLUMINA ss3628521859 Oct 12, 2018 (152)
65 ILLUMINA ss3638379382 Oct 12, 2018 (152)
66 ILLUMINA ss3643339386 Oct 12, 2018 (152)
67 URBANLAB ss3651169127 Oct 12, 2018 (152)
68 EGCUT_WGS ss3685717183 Jul 13, 2019 (153)
69 EVA_DECODE ss3708096760 Jul 13, 2019 (153)
70 ACPOP ss3743887895 Jul 13, 2019 (153)
71 EVA ss3759319811 Jul 13, 2019 (153)
72 PACBIO ss3788814401 Jul 13, 2019 (153)
73 PACBIO ss3793682524 Jul 13, 2019 (153)
74 PACBIO ss3798568962 Jul 13, 2019 (153)
75 KHV_HUMAN_GENOMES ss3822484966 Jul 13, 2019 (153)
76 EVA ss3835964431 Apr 27, 2020 (154)
77 EVA ss3841610545 Apr 27, 2020 (154)
78 EVA ss3847125364 Apr 27, 2020 (154)
79 SGDP_PRJ ss3890438759 Apr 27, 2020 (154)
80 KRGDB ss3940824204 Apr 27, 2020 (154)
81 KOGIC ss3983537906 Apr 27, 2020 (154)
82 EVA ss4017877836 Apr 27, 2021 (155)
83 TOPMED ss5107469731 Apr 27, 2021 (155)
84 TOMMO_GENOMICS ss5232394492 Apr 27, 2021 (155)
85 1000Genomes NC_000022.10 - 29782433 Oct 12, 2018 (152)
86 The Avon Longitudinal Study of Parents and Children NC_000022.10 - 29782433 Oct 12, 2018 (152)
87 Genetic variation in the Estonian population NC_000022.10 - 29782433 Oct 12, 2018 (152)
88 The Danish reference pan genome NC_000022.10 - 29782433 Apr 27, 2020 (154)
89 gnomAD - Genomes NC_000022.11 - 29386444 Apr 27, 2021 (155)
90 Genome of the Netherlands Release 5 NC_000022.10 - 29782433 Apr 27, 2020 (154)
91 HapMap NC_000022.11 - 29386444 Apr 27, 2020 (154)
92 KOREAN population from KRGDB NC_000022.10 - 29782433 Apr 27, 2020 (154)
93 Korean Genome Project NC_000022.11 - 29386444 Apr 27, 2020 (154)
94 Northern Sweden NC_000022.10 - 29782433 Jul 13, 2019 (153)
95 Qatari NC_000022.10 - 29782433 Apr 27, 2020 (154)
96 SGDP_PRJ NC_000022.10 - 29782433 Apr 27, 2020 (154)
97 Siberian NC_000022.10 - 29782433 Apr 27, 2020 (154)
98 8.3KJPN NC_000022.10 - 29782433 Apr 27, 2021 (155)
99 TopMed NC_000022.11 - 29386444 Apr 27, 2021 (155)
100 UK 10K study - Twins NC_000022.10 - 29782433 Oct 12, 2018 (152)
101 A Vietnamese Genetic Variation Database NC_000022.10 - 29782433 Jul 13, 2019 (153)
102 ALFA NC_000022.11 - 29386444 Apr 27, 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)
rs17534747 Oct 07, 2004 (123)
rs58431087 Feb 27, 2009 (130)
Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
ss78636846 NC_000022.8:28106986:A:C NC_000022.11:29386443:A:C (self)
ss112602595, ss114128293, ss117386625, ss167828822, ss169084037, ss171911862, ss204072250, ss208828401, ss244260799, ss255876181, ss283617076, ss292750586, ss1699366467, ss1713737060, ss3643339386 NC_000022.9:28112432:A:C NC_000022.11:29386443:A:C (self)
80510508, 44530763, 31455431, 5896748, 19843968, 48001598, 17172760, 20905540, 42455739, 11335805, 90363799, 44530763, 9825854, ss228654080, ss238049140, ss244172938, ss537442372, ss566605124, ss662536408, ss995297368, ss1082620323, ss1366965954, ss1429241810, ss1579731809, ss1639887829, ss1682881862, ss1809766005, ss1938863618, ss1969262030, ss2030203595, ss2158819451, ss2413864355, ss2629600273, ss2633871481, ss2704570388, ss2973818469, ss3019219969, ss3352813243, ss3628521859, ss3638379382, ss3685717183, ss3743887895, ss3759319811, ss3788814401, ss3793682524, ss3798568962, ss3835964431, ss3841610545, ss3890438759, ss3940824204, ss4017877836, ss5232394492 NC_000022.10:29782432:A:C NC_000022.11:29386443:A:C (self)
568534048, 2243144, 39915907, 238949812, 382578678, 10216760833, ss2246926911, ss3028939352, ss3375881405, ss3651169127, ss3708096760, ss3822484966, ss3847125364, ss3983537906, ss5107469731 NC_000022.11:29386443:A:C NC_000022.11:29386443:A:C (self)
ss13390851, ss17719365, ss21842233 NT_011520.9:9173001:A:C NC_000022.11:29386443:A:C (self)
ss27757, ss3200376, ss8292243, ss24556460, ss44308099, ss65723836, ss66136072, ss74878372, ss76148229, ss81434145, ss96120933, ss103852629, ss120244563, ss144220070, ss157116820, ss172640536, ss174265416 NT_011520.12:9173001:A:C NC_000022.11:29386443:A: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 rs715494

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.post596+ae089ad