Name: rs4657644
Published: September 21, 2022
License: Open Access

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 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr1:167168862 (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>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) (+ 19 more)
G=0.00004 (1/28256, 14KJPN)
G=0.1541 (987/6404, 1000G_30x)
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

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	190376	T=0.903281	G=0.096719
European	Sub	160326	T=0.918691	G=0.081309
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	6878	T=0.8944	G=0.1056

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").

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Study	Population	Group	Sample Size	Ref Allele	Alt Allele
TopMed	Global	Study-wide	264690	T=0.835978	G=0.164022
Allele Frequency Aggregator	Total	Global	190282	T=0.903312	G=0.096688
Allele Frequency Aggregator	European	Sub	160250	T=0.918733	G=0.081267
Allele Frequency Aggregator	African	Sub	9698	T=0.6247	G=0.3753
Allele Frequency Aggregator	Latin American 2	Sub	6892	T=0.9404	G=0.0596
Allele Frequency Aggregator	Other	Sub	6860	T=0.8945	G=0.1055
Allele Frequency Aggregator	South Asian	Sub	5042	T=0.9078	G=0.0922
Allele Frequency Aggregator	Latin American 1	Sub	840	T=0.839	G=0.161
Allele Frequency Aggregator	Asian	Sub	700	T=1.000	G=0.000
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
14KJPN	JAPANESE	Study-wide	28256	T=0.99996	G=0.00004
1000Genomes_30x	Global	Study-wide	6404	T=0.8459	G=0.1541
1000Genomes_30x	African	Sub	1786	T=0.6053	G=0.3947
1000Genomes_30x	Europe	Sub	1266	T=0.9202	G=0.0798
1000Genomes_30x	South Asian	Sub	1202	T=0.9126	G=0.0874
1000Genomes_30x	East Asian	Sub	1170	T=1.0000	G=0.0000
1000Genomes_30x	American	Sub	980	T=0.922	G=0.078
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

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.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_922250.3:n.	N/A	Intron Variant

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

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.p14 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

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#.

95 SubSNP, 21 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	ILLUMINA	ss2632588209	Nov 08, 2017 (151)
51	GNOMAD	ss2762317411	Nov 08, 2017 (151)
52	AFFY	ss2984883945	Nov 08, 2017 (151)
53	AFFY	ss2985529557	Nov 08, 2017 (151)
54	SWEGEN	ss2987896342	Nov 08, 2017 (151)
55	BIOINF_KMB_FNS_UNIBA	ss3023768874	Nov 08, 2017 (151)
56	CSHL	ss3343752771	Nov 08, 2017 (151)
57	ILLUMINA	ss3626231753	Oct 11, 2018 (152)
58	ILLUMINA	ss3630620317	Oct 11, 2018 (152)
59	ILLUMINA	ss3632913742	Oct 11, 2018 (152)
60	ILLUMINA	ss3633609256	Oct 11, 2018 (152)
61	ILLUMINA	ss3634356362	Oct 11, 2018 (152)
62	ILLUMINA	ss3635302626	Oct 11, 2018 (152)
63	ILLUMINA	ss3636035306	Oct 11, 2018 (152)
64	ILLUMINA	ss3637053125	Oct 11, 2018 (152)
65	ILLUMINA	ss3637793442	Oct 11, 2018 (152)
66	ILLUMINA	ss3638913324	Oct 11, 2018 (152)
67	ILLUMINA	ss3639768713	Oct 11, 2018 (152)
68	ILLUMINA	ss3640063716	Oct 11, 2018 (152)
69	ILLUMINA	ss3642802122	Oct 11, 2018 (152)
70	ILLUMINA	ss3643822050	Oct 11, 2018 (152)
71	ILLUMINA	ss3653653366	Oct 11, 2018 (152)
72	EGCUT_WGS	ss3655839310	Jul 12, 2019 (153)
73	EVA_DECODE	ss3687956487	Jul 12, 2019 (153)
74	ACPOP	ss3727564121	Jul 12, 2019 (153)
75	ILLUMINA	ss3744657245	Jul 12, 2019 (153)
76	EVA	ss3746917628	Jul 12, 2019 (153)
77	ILLUMINA	ss3772158305	Jul 12, 2019 (153)
78	KHV_HUMAN_GENOMES	ss3799918330	Jul 12, 2019 (153)
79	HGDP	ss3847352739	Apr 25, 2020 (154)
80	SGDP_PRJ	ss3850189682	Apr 25, 2020 (154)
81	KRGDB	ss3895422181	Apr 25, 2020 (154)
82	KOGIC	ss3945830748	Apr 25, 2020 (154)
83	EVA	ss3984831617	Apr 25, 2021 (155)
84	EVA	ss4016943467	Apr 25, 2021 (155)
85	TOPMED	ss4471401445	Apr 25, 2021 (155)
86	1000G_HIGH_COVERAGE	ss5244600892	Oct 12, 2022 (156)
87	EVA	ss5322612092	Oct 12, 2022 (156)
88	HUGCELL_USP	ss5445153880	Oct 12, 2022 (156)
89	1000G_HIGH_COVERAGE	ss5518083852	Oct 12, 2022 (156)
90	SANFORD_IMAGENETICS	ss5626767443	Oct 12, 2022 (156)
91	TOMMO_GENOMICS	ss5674201188	Oct 12, 2022 (156)
92	EVA	ss5799501910	Oct 12, 2022 (156)
93	EVA	ss5832788055	Oct 12, 2022 (156)
94	EVA	ss5910597220	Oct 12, 2022 (156)
95	EVA	ss5938567512	Oct 12, 2022 (156)
96	1000Genomes	NC_000001.10 - 167138099	Oct 11, 2018 (152)
97	1000Genomes_30x	NC_000001.11 - 167168862	Oct 12, 2022 (156)
98	The Avon Longitudinal Study of Parents and Children	NC_000001.10 - 167138099	Oct 11, 2018 (152)
99	Chileans	NC_000001.10 - 167138099	Apr 25, 2020 (154)
100	Genetic variation in the Estonian population	NC_000001.10 - 167138099	Oct 11, 2018 (152)
101	The Danish reference pan genome	NC_000001.10 - 167138099	Apr 25, 2020 (154)
102	gnomAD - Genomes	NC_000001.11 - 167168862	Apr 25, 2021 (155)
103	Genome of the Netherlands Release 5	NC_000001.10 - 167138099	Apr 25, 2020 (154)
104	HGDP-CEPH-db Supplement 1	NC_000001.9 - 165404723	Apr 25, 2020 (154)
105	HapMap	NC_000001.11 - 167168862	Apr 25, 2020 (154)
106	KOREAN population from KRGDB	NC_000001.10 - 167138099	Apr 25, 2020 (154)
107	Korean Genome Project	NC_000001.11 - 167168862	Apr 25, 2020 (154)
108	Northern Sweden	NC_000001.10 - 167138099	Jul 12, 2019 (153)
109	Ancient Sardinia genome-wide 1240k capture data generation and analysis	NC_000001.10 - 167138099	Apr 25, 2021 (155)
110	Qatari	NC_000001.10 - 167138099	Apr 25, 2020 (154)
111	SGDP_PRJ	NC_000001.10 - 167138099	Apr 25, 2020 (154)
112	Siberian	NC_000001.10 - 167138099	Apr 25, 2020 (154)
113	14KJPN	NC_000001.11 - 167168862	Oct 12, 2022 (156)
114	TopMed	NC_000001.11 - 167168862	Apr 25, 2021 (155)
115	UK 10K study - Twins	NC_000001.10 - 167138099	Oct 11, 2018 (152)
116	ALFA	NC_000001.11 - 167168862	Apr 25, 2021 (155)

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, 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, ss5322612092, ss5626767443, ss5799501910, ss5832788055, ss5938567512	NC_000001.10:167138098:T:G	NC_000001.11:167168861:T:G	(self)
5609787, 29596961, 196151, 2208749, 8038292, 35007780, 13577335108, ss2167250792, ss3023768874, ss3687956487, ss3799918330, ss3945830748, ss4471401445, ss5244600892, ss5445153880, ss5518083852, ss5674201188, ss5910597220	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)

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

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.

Choose placement

dbSNP Short Genetic Variations

Welcome to the Reference SNP (rs) Report

Reference SNP (rs) Report

rs4657644