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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.

rs4657644

Current Build 155

Released April 9, 2021

Organism
Homo sapiens
Position
chr1:167168862 (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
T>G
Variation Type
SNV Single Nucleotide Variation
Frequency
G=0.164022 (43415/264690, TOPMED)
G=0.096688 (18398/190282, ALFA)
G=0.165486 (23178/140060, GnomAD) (+ 17 more)
G=0.1488 (745/5008, 1000G)
G=0.0685 (307/4480, Estonian)
G=0.0893 (344/3854, ALSPAC)
G=0.0839 (311/3708, TWINSUK)
G=0.0003 (1/2922, KOREAN)
G=0.1161 (242/2084, HGDP_Stanford)
G=0.0005 (1/1832, Korea1K)
G=0.2301 (358/1556, HapMap)
G=0.074 (74/998, GoNL)
G=0.070 (44/626, Chileans)
G=0.103 (62/600, NorthernSweden)
G=0.204 (44/216, Qatari)
T=0.41 (41/100, SGDP_PRJ)
G=0.03 (2/68, Ancient Sardinia)
G=0.05 (2/40, GENOME_DK)
T=0.5 (3/6, Siberian)
G=0.5 (3/6, Siberian)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
LOC105371601 : 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 1 NC_000001.11:g.167168862T>G
GRCh37.p13 chr 1 NC_000001.10:g.167138099T>G
Gene: LOC105371601, uncharacterized LOC105371601 (plus strand)
Molecule type Change Amino acid[Codon] SO Term
LOC105371601 transcript XR_922250.2: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 190282 T=0.903312 G=0.096688
European Sub 160250 T=0.918733 G=0.081267
African Sub 9698 T=0.6247 G=0.3753
African Others Sub 348 T=0.520 G=0.480
African American Sub 9350 T=0.6286 G=0.3714
Asian Sub 700 T=1.000 G=0.000
East Asian Sub 554 T=1.000 G=0.000
Other Asian Sub 146 T=1.000 G=0.000
Latin American 1 Sub 840 T=0.839 G=0.161
Latin American 2 Sub 6892 T=0.9404 G=0.0596
South Asian Sub 5042 T=0.9078 G=0.0922
Other Sub 6860 T=0.8945 G=0.1055


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=0.835978 G=0.164022
gnomAD - Genomes Global Study-wide 140060 T=0.834514 G=0.165486
gnomAD - Genomes European Sub 75902 T=0.91619 G=0.08381
gnomAD - Genomes African Sub 41894 T=0.64086 G=0.35914
gnomAD - Genomes American Sub 13656 T=0.91484 G=0.08516
gnomAD - Genomes Ashkenazi Jewish Sub 3324 T=0.9079 G=0.0921
gnomAD - Genomes East Asian Sub 3132 T=0.9974 G=0.0026
gnomAD - Genomes Other Sub 2152 T=0.8634 G=0.1366
1000Genomes Global Study-wide 5008 T=0.8512 G=0.1488
1000Genomes African Sub 1322 T=0.6021 G=0.3979
1000Genomes East Asian Sub 1008 T=1.0000 G=0.0000
1000Genomes Europe Sub 1006 T=0.9155 G=0.0845
1000Genomes South Asian Sub 978 T=0.915 G=0.085
1000Genomes American Sub 694 T=0.927 G=0.073
Genetic variation in the Estonian population Estonian Study-wide 4480 T=0.9315 G=0.0685
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 T=0.9107 G=0.0893
UK 10K study - Twins TWIN COHORT Study-wide 3708 T=0.9161 G=0.0839
KOREAN population from KRGDB KOREAN Study-wide 2922 T=0.9997 G=0.0003
HGDP-CEPH-db Supplement 1 Global Study-wide 2084 T=0.8839 G=0.1161
HGDP-CEPH-db Supplement 1 Est_Asia Sub 470 T=0.991 G=0.009
HGDP-CEPH-db Supplement 1 Central_South_Asia Sub 414 T=0.903 G=0.097
HGDP-CEPH-db Supplement 1 Middle_Est Sub 350 T=0.860 G=0.140
HGDP-CEPH-db Supplement 1 Europe Sub 320 T=0.912 G=0.087
HGDP-CEPH-db Supplement 1 Africa Sub 242 T=0.508 G=0.492
HGDP-CEPH-db Supplement 1 America Sub 216 T=0.991 G=0.009
HGDP-CEPH-db Supplement 1 Oceania Sub 72 T=1.00 G=0.00
Korean Genome Project KOREAN Study-wide 1832 T=0.9995 G=0.0005
HapMap Global Study-wide 1556 T=0.7699 G=0.2301
HapMap African Sub 692 T=0.598 G=0.402
HapMap American Sub 598 T=0.885 G=0.115
HapMap Europe Sub 176 T=0.938 G=0.062
HapMap Asian Sub 90 T=1.00 G=0.00
Genome of the Netherlands Release 5 Genome of the Netherlands Study-wide 998 T=0.926 G=0.074
Chileans Chilean Study-wide 626 T=0.930 G=0.070
Northern Sweden ACPOP Study-wide 600 T=0.897 G=0.103
Qatari Global Study-wide 216 T=0.796 G=0.204
SGDP_PRJ Global Study-wide 100 T=0.41 G=0.59
Ancient Sardinia genome-wide 1240k capture data generation and analysis Global Study-wide 68 T=0.97 G=0.03
The Danish reference pan genome Danish Study-wide 40 T=0.95 G=0.05
Siberian Global Study-wide 6 T=0.5 G=0.5
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= G
GRCh38.p13 chr 1 NC_000001.11:g.167168862= NC_000001.11:g.167168862T>G
GRCh37.p13 chr 1 NC_000001.10:g.167138099= NC_000001.10:g.167138099T>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#.

87 SubSNP, 19 Frequency submissions
No Submitter Submission ID Date (Build)
1 WI_SSAHASNP ss6411133 Feb 20, 2003 (111)
2 PERLEGEN ss23145065 Sep 20, 2004 (123)
3 ILLUMINA ss67354129 Dec 01, 2006 (127)
4 ILLUMINA ss67744006 Dec 01, 2006 (127)
5 ILLUMINA ss68232516 Dec 12, 2006 (127)
6 PERLEGEN ss68783610 May 18, 2007 (127)
7 ILLUMINA ss70813598 May 24, 2008 (130)
8 ILLUMINA ss71394181 May 18, 2007 (127)
9 ILLUMINA ss75619294 Dec 07, 2007 (129)
10 KRIBB_YJKIM ss84306604 Dec 14, 2007 (130)
11 HGSV ss85263897 Dec 14, 2007 (130)
12 ILLUMINA ss154305036 Dec 01, 2009 (131)
13 ILLUMINA ss159481846 Dec 01, 2009 (131)
14 ILLUMINA ss160694758 Dec 01, 2009 (131)
15 COMPLETE_GENOMICS ss167240036 Jul 04, 2010 (132)
16 ILLUMINA ss173770408 Jul 04, 2010 (132)
17 BUSHMAN ss199198617 Jul 04, 2010 (132)
18 BCM-HGSC-SUB ss205308002 Jul 04, 2010 (132)
19 1000GENOMES ss210661852 Jul 14, 2010 (132)
20 1000GENOMES ss218698163 Jul 14, 2010 (132)
21 1000GENOMES ss230767058 Jul 14, 2010 (132)
22 ILLUMINA ss480991927 May 04, 2012 (137)
23 ILLUMINA ss481012492 May 04, 2012 (137)
24 ILLUMINA ss481993150 Sep 08, 2015 (146)
25 ILLUMINA ss485290850 May 04, 2012 (137)
26 ILLUMINA ss537254046 Sep 08, 2015 (146)
27 TISHKOFF ss554807970 Apr 25, 2013 (138)
28 ILLUMINA ss778541111 Sep 08, 2015 (146)
29 ILLUMINA ss783091315 Sep 08, 2015 (146)
30 ILLUMINA ss784048713 Sep 08, 2015 (146)
31 ILLUMINA ss832349788 Sep 08, 2015 (146)
32 ILLUMINA ss832993273 Jul 12, 2019 (153)
33 ILLUMINA ss833997740 Sep 08, 2015 (146)
34 EVA-GONL ss975776340 Aug 21, 2014 (142)
35 JMKIDD_LAB ss1068337141 Aug 21, 2014 (142)
36 1000GENOMES ss1293281306 Aug 21, 2014 (142)
37 DDI ss1426006452 Apr 01, 2015 (144)
38 EVA_GENOME_DK ss1574452541 Apr 01, 2015 (144)
39 EVA_DECODE ss1585161270 Apr 01, 2015 (144)
40 EVA_UK10K_ALSPAC ss1601403165 Apr 01, 2015 (144)
41 EVA_UK10K_TWINSUK ss1644397198 Apr 01, 2015 (144)
42 EVA_SVP ss1712378614 Apr 01, 2015 (144)
43 ILLUMINA ss1751879367 Sep 08, 2015 (146)
44 HAMMER_LAB ss1795217918 Sep 08, 2015 (146)
45 WEILL_CORNELL_DGM ss1919012581 Feb 12, 2016 (147)
46 GENOMED ss1966889756 Jul 19, 2016 (147)
47 JJLAB ss2020021871 Sep 14, 2016 (149)
48 USC_VALOUEV ss2148049108 Dec 20, 2016 (150)
49 HUMAN_LONGEVITY ss2167250792 Dec 20, 2016 (150)
50 TOPMED ss2329786910 Dec 20, 2016 (150)
51 ILLUMINA ss2632588209 Nov 08, 2017 (151)
52 GNOMAD ss2762317411 Nov 08, 2017 (151)
53 AFFY ss2984883945 Nov 08, 2017 (151)
54 AFFY ss2985529557 Nov 08, 2017 (151)
55 SWEGEN ss2987896342 Nov 08, 2017 (151)
56 BIOINF_KMB_FNS_UNIBA ss3023768874 Nov 08, 2017 (151)
57 TOPMED ss3094436262 Nov 08, 2017 (151)
58 CSHL ss3343752771 Nov 08, 2017 (151)
59 ILLUMINA ss3626231753 Oct 11, 2018 (152)
60 ILLUMINA ss3630620317 Oct 11, 2018 (152)
61 ILLUMINA ss3632913742 Oct 11, 2018 (152)
62 ILLUMINA ss3633609256 Oct 11, 2018 (152)
63 ILLUMINA ss3634356362 Oct 11, 2018 (152)
64 ILLUMINA ss3635302626 Oct 11, 2018 (152)
65 ILLUMINA ss3636035306 Oct 11, 2018 (152)
66 ILLUMINA ss3637053125 Oct 11, 2018 (152)
67 ILLUMINA ss3637793442 Oct 11, 2018 (152)
68 ILLUMINA ss3638913324 Oct 11, 2018 (152)
69 ILLUMINA ss3639768713 Oct 11, 2018 (152)
70 ILLUMINA ss3640063716 Oct 11, 2018 (152)
71 ILLUMINA ss3642802122 Oct 11, 2018 (152)
72 ILLUMINA ss3643822050 Oct 11, 2018 (152)
73 ILLUMINA ss3653653366 Oct 11, 2018 (152)
74 EGCUT_WGS ss3655839310 Jul 12, 2019 (153)
75 EVA_DECODE ss3687956487 Jul 12, 2019 (153)
76 ACPOP ss3727564121 Jul 12, 2019 (153)
77 ILLUMINA ss3744657245 Jul 12, 2019 (153)
78 EVA ss3746917628 Jul 12, 2019 (153)
79 ILLUMINA ss3772158305 Jul 12, 2019 (153)
80 KHV_HUMAN_GENOMES ss3799918330 Jul 12, 2019 (153)
81 HGDP ss3847352739 Apr 25, 2020 (154)
82 SGDP_PRJ ss3850189682 Apr 25, 2020 (154)
83 KRGDB ss3895422181 Apr 25, 2020 (154)
84 KOGIC ss3945830748 Apr 25, 2020 (154)
85 EVA ss3984831617 Apr 25, 2021 (155)
86 EVA ss4016943467 Apr 25, 2021 (155)
87 TOPMED ss4471401445 Apr 25, 2021 (155)
88 1000Genomes NC_000001.10 - 167138099 Oct 11, 2018 (152)
89 The Avon Longitudinal Study of Parents and Children NC_000001.10 - 167138099 Oct 11, 2018 (152)
90 Chileans NC_000001.10 - 167138099 Apr 25, 2020 (154)
91 Genetic variation in the Estonian population NC_000001.10 - 167138099 Oct 11, 2018 (152)
92 The Danish reference pan genome NC_000001.10 - 167138099 Apr 25, 2020 (154)
93 gnomAD - Genomes NC_000001.11 - 167168862 Apr 25, 2021 (155)
94 Genome of the Netherlands Release 5 NC_000001.10 - 167138099 Apr 25, 2020 (154)
95 HGDP-CEPH-db Supplement 1 NC_000001.9 - 165404723 Apr 25, 2020 (154)
96 HapMap NC_000001.11 - 167168862 Apr 25, 2020 (154)
97 KOREAN population from KRGDB NC_000001.10 - 167138099 Apr 25, 2020 (154)
98 Korean Genome Project NC_000001.11 - 167168862 Apr 25, 2020 (154)
99 Northern Sweden NC_000001.10 - 167138099 Jul 12, 2019 (153)
100 Ancient Sardinia genome-wide 1240k capture data generation and analysis NC_000001.10 - 167138099 Apr 25, 2021 (155)
101 Qatari NC_000001.10 - 167138099 Apr 25, 2020 (154)
102 SGDP_PRJ NC_000001.10 - 167138099 Apr 25, 2020 (154)
103 Siberian NC_000001.10 - 167138099 Apr 25, 2020 (154)
104 TopMed NC_000001.11 - 167168862 Apr 25, 2021 (155)
105 UK 10K study - Twins NC_000001.10 - 167138099 Oct 11, 2018 (152)
106 ALFA NC_000001.11 - 167168862 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)
rs57769868 May 24, 2008 (130)
rs111191400 Aug 21, 2014 (142)
Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
ss85263897, ss3638913324, ss3639768713, ss3643822050 NC_000001.8:163869756:T:G NC_000001.11:167168861:T:G (self)
30631, ss167240036, ss199198617, ss205308002, ss210661852, ss480991927, ss1585161270, ss1712378614, ss3642802122, ss3847352739 NC_000001.9:165404722:T:G NC_000001.11:167168861:T:G (self)
4085222, 2228409, 23584, 1577558, 1745228, 969105, 2599575, 848986, 57544, 1054511, 2206662, 565462, 2228409, ss218698163, ss230767058, ss481012492, ss481993150, ss485290850, ss537254046, ss554807970, ss778541111, ss783091315, ss784048713, ss832349788, ss832993273, ss833997740, ss975776340, ss1068337141, ss1293281306, ss1426006452, ss1574452541, ss1601403165, ss1644397198, ss1751879367, ss1795217918, ss1919012581, ss1966889756, ss2020021871, ss2148049108, ss2329786910, ss2632588209, ss2762317411, ss2984883945, ss2985529557, ss2987896342, ss3343752771, ss3626231753, ss3630620317, ss3632913742, ss3633609256, ss3634356362, ss3635302626, ss3636035306, ss3637053125, ss3637793442, ss3640063716, ss3653653366, ss3655839310, ss3727564121, ss3744657245, ss3746917628, ss3772158305, ss3850189682, ss3895422181, ss3984831617, ss4016943467 NC_000001.10:167138098:T:G NC_000001.11:167168861:T:G (self)
29596961, 196151, 2208749, 21973353, 35007780, 13577335108, ss2167250792, ss3023768874, ss3094436262, ss3687956487, ss3799918330, ss3945830748, ss4471401445 NC_000001.11:167168861:T:G NC_000001.11:167168861:T:G (self)
ss6411133, ss23145065, ss67354129, ss67744006, ss68232516, ss68783610, ss70813598, ss71394181, ss75619294, ss84306604, ss154305036, ss159481846, ss160694758, ss173770408 NT_004487.19:18626740:T:G NC_000001.11:167168861:T:G (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 rs4657644

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