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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.

rs230488

Current Build 155

Released April 9, 2021

Organism
Homo sapiens
Position
chr4:102467408 (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 / A>G / A>T
Variation Type
SNV Single Nucleotide Variation
Frequency
A=0.248347 (65735/264690, TOPMED)
A=0.233644 (32734/140102, GnomAD)
A=0.24083 (18952/78694, PAGE_STUDY) (+ 16 more)
A=0.24752 (18350/74136, ALFA)
A=0.16187 (2713/16760, 8.3KJPN)
A=0.2532 (1268/5008, 1000G)
A=0.2098 (940/4480, Estonian)
A=0.2667 (1028/3854, ALSPAC)
A=0.2694 (999/3708, TWINSUK)
A=0.1898 (556/2930, KOREAN)
A=0.1960 (359/1832, Korea1K)
A=0.259 (258/998, GoNL)
A=0.230 (138/600, NorthernSweden)
A=0.173 (78/452, SGDP_PRJ)
A=0.185 (57/308, HapMap)
A=0.301 (65/216, Qatari)
A=0.165 (35/212, Vietnamese)
A=0.36 (18/50, Siberian)
A=0.28 (11/40, GENOME_DK)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
LOC105377621 : Intron 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 4 NC_000004.12:g.102467408A>C
GRCh38.p13 chr 4 NC_000004.12:g.102467408A>G
GRCh38.p13 chr 4 NC_000004.12:g.102467408A>T
GRCh37.p13 chr 4 NC_000004.11:g.103388565A>C
GRCh37.p13 chr 4 NC_000004.11:g.103388565A>G
GRCh37.p13 chr 4 NC_000004.11:g.103388565A>T
Gene: LOC105377621, uncharacterized LOC105377621 (minus strand)
Molecule type Change Amino acid[Codon] SO Term
LOC105377621 transcript NR_136202.1:n. 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

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 74136 A=0.24752 G=0.75248
European Sub 58946 A=0.25744 G=0.74256
African Sub 8222 A=0.1486 G=0.8514
African Others Sub 274 A=0.135 G=0.865
African American Sub 7948 A=0.1491 G=0.8509
Asian Sub 532 A=0.207 G=0.793
East Asian Sub 464 A=0.209 G=0.791
Other Asian Sub 68 A=0.19 G=0.81
Latin American 1 Sub 536 A=0.239 G=0.761
Latin American 2 Sub 926 A=0.383 G=0.617
South Asian Sub 186 A=0.452 G=0.548
Other Sub 4788 A=0.2665 G=0.7335


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=0.248347 G=0.751653
gnomAD - Genomes Global Study-wide 140102 A=0.233644 G=0.766356
gnomAD - Genomes European Sub 75880 A=0.24972 G=0.75028
gnomAD - Genomes African Sub 41976 A=0.14909 G=0.85091
gnomAD - Genomes American Sub 13650 A=0.39722 G=0.60278
gnomAD - Genomes Ashkenazi Jewish Sub 3322 A=0.2664 G=0.7336
gnomAD - Genomes East Asian Sub 3124 A=0.2129 G=0.7871
gnomAD - Genomes Other Sub 2150 A=0.2581 G=0.7419
The PAGE Study Global Study-wide 78694 A=0.24083 G=0.75917
The PAGE Study AfricanAmerican Sub 32514 A=0.15252 G=0.84748
The PAGE Study Mexican Sub 10806 A=0.40857 G=0.59143
The PAGE Study Asian Sub 8318 A=0.1752 G=0.8248
The PAGE Study PuertoRican Sub 7918 A=0.3084 G=0.6916
The PAGE Study NativeHawaiian Sub 4534 A=0.2100 G=0.7900
The PAGE Study Cuban Sub 4230 A=0.2669 G=0.7331
The PAGE Study Dominican Sub 3828 A=0.2364 G=0.7636
The PAGE Study CentralAmerican Sub 2450 A=0.4322 G=0.5678
The PAGE Study SouthAmerican Sub 1980 A=0.4828 G=0.5172
The PAGE Study NativeAmerican Sub 1260 A=0.2881 G=0.7119
The PAGE Study SouthAsian Sub 856 A=0.368 G=0.632
8.3KJPN JAPANESE Study-wide 16760 A=0.16187 G=0.83813
1000Genomes Global Study-wide 5008 A=0.2532 G=0.7468
1000Genomes African Sub 1322 A=0.1188 G=0.8812
1000Genomes East Asian Sub 1008 A=0.1954 G=0.8046
1000Genomes Europe Sub 1006 A=0.2505 G=0.7495
1000Genomes South Asian Sub 978 A=0.352 G=0.648
1000Genomes American Sub 694 A=0.458 G=0.542
Genetic variation in the Estonian population Estonian Study-wide 4480 A=0.2098 G=0.7902
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 A=0.2667 G=0.7333
UK 10K study - Twins TWIN COHORT Study-wide 3708 A=0.2694 G=0.7306
KOREAN population from KRGDB KOREAN Study-wide 2930 A=0.1898 C=0.0000, G=0.8102, T=0.0000
Korean Genome Project KOREAN Study-wide 1832 A=0.1960 G=0.8040
Genome of the Netherlands Release 5 Genome of the Netherlands Study-wide 998 A=0.259 G=0.741
Northern Sweden ACPOP Study-wide 600 A=0.230 G=0.770
SGDP_PRJ Global Study-wide 452 A=0.173 G=0.827
HapMap Global Study-wide 308 A=0.185 G=0.815
HapMap African Sub 114 A=0.079 G=0.921
HapMap American Sub 114 A=0.298 G=0.702
HapMap Asian Sub 80 A=0.17 G=0.82
Qatari Global Study-wide 216 A=0.301 G=0.699
A Vietnamese Genetic Variation Database Global Study-wide 212 A=0.165 G=0.835
Siberian Global Study-wide 50 A=0.36 G=0.64
The Danish reference pan genome Danish Study-wide 40 A=0.28 G=0.72
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 G T
GRCh38.p13 chr 4 NC_000004.12:g.102467408= NC_000004.12:g.102467408A>C NC_000004.12:g.102467408A>G NC_000004.12:g.102467408A>T
GRCh37.p13 chr 4 NC_000004.11:g.103388565= NC_000004.11:g.103388565A>C NC_000004.11:g.103388565A>G NC_000004.11:g.103388565A>T
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#.

75 SubSNP, 19 Frequency submissions
No Submitter Submission ID Date (Build)
1 KWOK ss298173 Jul 12, 2000 (79)
2 SC_JCM ss724671 Aug 11, 2000 (85)
3 KWOK ss1043232 Oct 04, 2000 (86)
4 KWOK ss1949110 Oct 18, 2000 (89)
5 PERLEGEN ss68906785 May 18, 2007 (127)
6 KRIBB_YJKIM ss80750571 Dec 15, 2007 (130)
7 BCMHGSC_JDW ss92710625 Mar 24, 2008 (129)
8 BGI ss105849500 Feb 05, 2009 (130)
9 1000GENOMES ss108187984 Jan 23, 2009 (130)
10 ENSEMBL ss139792315 Dec 01, 2009 (131)
11 ILLUMINA ss160534394 Dec 01, 2009 (131)
12 BCM-HGSC-SUB ss206524486 Jul 04, 2010 (132)
13 1000GENOMES ss221111173 Jul 14, 2010 (132)
14 1000GENOMES ss232524174 Jul 14, 2010 (132)
15 1000GENOMES ss239786863 Jul 15, 2010 (132)
16 BL ss253387279 May 09, 2011 (134)
17 GMI ss277853024 May 04, 2012 (137)
18 GMI ss284971965 Apr 25, 2013 (138)
19 PJP ss293151875 May 09, 2011 (134)
20 ILLUMINA ss481351963 Sep 08, 2015 (146)
21 ILLUMINA ss483457335 May 04, 2012 (137)
22 ILLUMINA ss484664024 May 04, 2012 (137)
23 ILLUMINA ss535667222 Sep 08, 2015 (146)
24 TISHKOFF ss557735793 Apr 25, 2013 (138)
25 SSMP ss651539146 Apr 25, 2013 (138)
26 ILLUMINA ss780284613 Sep 08, 2015 (146)
27 ILLUMINA ss782172041 Sep 08, 2015 (146)
28 ILLUMINA ss835770964 Sep 08, 2015 (146)
29 EVA-GONL ss980475193 Aug 21, 2014 (142)
30 JMKIDD_LAB ss1071805548 Aug 21, 2014 (142)
31 1000GENOMES ss1311066258 Aug 21, 2014 (142)
32 HAMMER_LAB ss1397384125 Sep 08, 2015 (146)
33 DDI ss1429990349 Apr 01, 2015 (144)
34 EVA_GENOME_DK ss1580697096 Apr 01, 2015 (144)
35 EVA_UK10K_ALSPAC ss1610785630 Apr 01, 2015 (144)
36 EVA_UK10K_TWINSUK ss1653779663 Apr 01, 2015 (144)
37 HAMMER_LAB ss1801941210 Sep 08, 2015 (146)
38 WEILL_CORNELL_DGM ss1923714488 Feb 12, 2016 (147)
39 ILLUMINA ss1958708603 Feb 12, 2016 (147)
40 GENOMED ss1969822296 Jul 19, 2016 (147)
41 JJLAB ss2022443304 Sep 14, 2016 (149)
42 USC_VALOUEV ss2150572515 Dec 20, 2016 (150)
43 HUMAN_LONGEVITY ss2265608886 Dec 20, 2016 (150)
44 TOPMED ss2433430141 Dec 20, 2016 (150)
45 SYSTEMSBIOZJU ss2625720159 Nov 08, 2017 (151)
46 ILLUMINA ss2634157381 Nov 08, 2017 (151)
47 GRF ss2706049633 Nov 08, 2017 (151)
48 ILLUMINA ss2711012243 Nov 08, 2017 (151)
49 GNOMAD ss2813102661 Nov 08, 2017 (151)
50 SWEGEN ss2995246819 Nov 08, 2017 (151)
51 ILLUMINA ss3022400522 Nov 08, 2017 (151)
52 BIOINF_KMB_FNS_UNIBA ss3024997278 Nov 08, 2017 (151)
53 CSHL ss3345872770 Nov 08, 2017 (151)
54 TOPMED ss3437813571 Nov 08, 2017 (151)
55 ILLUMINA ss3629030239 Oct 12, 2018 (152)
56 ILLUMINA ss3632091588 Oct 12, 2018 (152)
57 ILLUMINA ss3636668687 Oct 12, 2018 (152)
58 ILLUMINA ss3642353519 Oct 12, 2018 (152)
59 URBANLAB ss3647807674 Oct 12, 2018 (152)
60 ILLUMINA ss3652887672 Oct 12, 2018 (152)
61 EGCUT_WGS ss3663144635 Jul 13, 2019 (153)
62 EVA_DECODE ss3712700528 Jul 13, 2019 (153)
63 ILLUMINA ss3726157440 Jul 13, 2019 (153)
64 ACPOP ss3731442120 Jul 13, 2019 (153)
65 EVA ss3762192362 Jul 13, 2019 (153)
66 PAGE_CC ss3771143879 Jul 13, 2019 (153)
67 KHV_HUMAN_GENOMES ss3805340846 Jul 13, 2019 (153)
68 EVA ss3828715424 Apr 26, 2020 (154)
69 EVA ss3837798913 Apr 26, 2020 (154)
70 EVA ss3843237437 Apr 26, 2020 (154)
71 SGDP_PRJ ss3859656621 Apr 26, 2020 (154)
72 KRGDB ss3905935258 Apr 26, 2020 (154)
73 KOGIC ss3954780371 Apr 26, 2020 (154)
74 TOPMED ss4625411649 Apr 26, 2021 (155)
75 TOMMO_GENOMICS ss5167171987 Apr 26, 2021 (155)
76 1000Genomes NC_000004.11 - 103388565 Oct 12, 2018 (152)
77 The Avon Longitudinal Study of Parents and Children NC_000004.11 - 103388565 Oct 12, 2018 (152)
78 Genetic variation in the Estonian population NC_000004.11 - 103388565 Oct 12, 2018 (152)
79 The Danish reference pan genome NC_000004.11 - 103388565 Apr 26, 2020 (154)
80 gnomAD - Genomes NC_000004.12 - 102467408 Apr 26, 2021 (155)
81 Genome of the Netherlands Release 5 NC_000004.11 - 103388565 Apr 26, 2020 (154)
82 HapMap NC_000004.12 - 102467408 Apr 26, 2020 (154)
83 KOREAN population from KRGDB NC_000004.11 - 103388565 Apr 26, 2020 (154)
84 Korean Genome Project NC_000004.12 - 102467408 Apr 26, 2020 (154)
85 Northern Sweden NC_000004.11 - 103388565 Jul 13, 2019 (153)
86 The PAGE Study NC_000004.12 - 102467408 Jul 13, 2019 (153)
87 Qatari NC_000004.11 - 103388565 Apr 26, 2020 (154)
88 SGDP_PRJ NC_000004.11 - 103388565 Apr 26, 2020 (154)
89 Siberian NC_000004.11 - 103388565 Apr 26, 2020 (154)
90 8.3KJPN NC_000004.11 - 103388565 Apr 26, 2021 (155)
91 TopMed NC_000004.12 - 102467408 Apr 26, 2021 (155)
92 UK 10K study - Twins NC_000004.11 - 103388565 Oct 12, 2018 (152)
93 A Vietnamese Genetic Variation Database NC_000004.11 - 103388565 Jul 13, 2019 (153)
94 ALFA NC_000004.12 - 102467408 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)
rs553698 Sep 19, 2000 (85)
rs1313891 Nov 09, 2000 (89)
rs58992372 May 25, 2008 (130)
Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
13112652, ss3905935258 NC_000004.11:103388564:A:C NC_000004.12:102467407:A:C (self)
ss92710625, ss108187984, ss206524486, ss253387279, ss277853024, ss284971965, ss293151875, ss484664024, ss1397384125 NC_000004.10:103607588:G:G NC_000004.12:102467407:A:G (self)
22511739, 12526360, 8882883, 6862035, 5538206, 13112652, 4726985, 5756418, 11673601, 3088869, 25141294, 12526360, 2755323, ss221111173, ss232524174, ss239786863, ss481351963, ss483457335, ss535667222, ss557735793, ss651539146, ss780284613, ss782172041, ss835770964, ss980475193, ss1071805548, ss1311066258, ss1429990349, ss1580697096, ss1610785630, ss1653779663, ss1801941210, ss1923714488, ss1958708603, ss1969822296, ss2022443304, ss2150572515, ss2433430141, ss2625720159, ss2634157381, ss2706049633, ss2711012243, ss2813102661, ss2995246819, ss3022400522, ss3345872770, ss3629030239, ss3632091588, ss3636668687, ss3642353519, ss3652887672, ss3663144635, ss3731442120, ss3762192362, ss3828715424, ss3837798913, ss3859656621, ss3905935258, ss5167171987 NC_000004.11:103388564:A:G NC_000004.12:102467407:A:G (self)
159471825, 2674305, 11158372, 365348, 289289804, 462789205, 3630099502, ss2265608886, ss3024997278, ss3437813571, ss3647807674, ss3712700528, ss3726157440, ss3771143879, ss3805340846, ss3843237437, ss3954780371, ss4625411649 NC_000004.12:102467407:A:G NC_000004.12:102467407:A:G (self)
ss298173, ss724671, ss1043232, ss1949110, ss68906785, ss80750571, ss105849500, ss139792315, ss160534394 NT_016354.19:27936285:A:G NC_000004.12:102467407:A:G (self)
13112652, ss3905935258 NC_000004.11:103388564:A:T NC_000004.12:102467407:A:T (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 rs230488

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