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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.

rs4648352

Current Build 155

Released April 9, 2021

Organism
Homo sapiens
Position
chr1:2924348 (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
G>A
Variation Type
SNV Single Nucleotide Variation
Frequency
A=0.326106 (86317/264690, TOPMED)
A=0.318332 (44592/140080, GnomAD)
A=0.29481 (5569/18890, ALFA) (+ 14 more)
A=0.26271 (4403/16760, 8.3KJPN)
A=0.3427 (1716/5008, 1000G)
A=0.3187 (1428/4480, Estonian)
A=0.2208 (851/3854, ALSPAC)
A=0.2168 (804/3708, TWINSUK)
A=0.2328 (682/2930, KOREAN)
A=0.2391 (438/1832, Korea1K)
A=0.221 (221/998, GoNL)
A=0.308 (185/600, NorthernSweden)
G=0.341 (116/340, SGDP_PRJ)
A=0.306 (66/216, Qatari)
A=0.181 (39/216, Vietnamese)
A=0.25 (10/40, GENOME_DK)
G=0.47 (15/32, Siberian)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
None
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.2924348G>A
GRCh37.p13 chr 1 NC_000001.10:g.2840913G>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 18890 G=0.70519 A=0.29481
European Sub 14286 G=0.74437 A=0.25563
African Sub 2946 G=0.5458 A=0.4542
African Others Sub 114 G=0.570 A=0.430
African American Sub 2832 G=0.5448 A=0.4552
Asian Sub 112 G=0.821 A=0.179
East Asian Sub 86 G=0.79 A=0.21
Other Asian Sub 26 G=0.92 A=0.08
Latin American 1 Sub 146 G=0.685 A=0.315
Latin American 2 Sub 610 G=0.580 A=0.420
South Asian Sub 98 G=0.63 A=0.37
Other Sub 692 G=0.681 A=0.319


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 G=0.673894 A=0.326106
gnomAD - Genomes Global Study-wide 140080 G=0.681668 A=0.318332
gnomAD - Genomes European Sub 75894 G=0.75428 A=0.24572
gnomAD - Genomes African Sub 41952 G=0.53852 A=0.46148
gnomAD - Genomes American Sub 13636 G=0.66486 A=0.33514
gnomAD - Genomes Ashkenazi Jewish Sub 3320 G=0.7633 A=0.2367
gnomAD - Genomes East Asian Sub 3124 G=0.8095 A=0.1905
gnomAD - Genomes Other Sub 2154 G=0.7066 A=0.2934
8.3KJPN JAPANESE Study-wide 16760 G=0.73729 A=0.26271
1000Genomes Global Study-wide 5008 G=0.6573 A=0.3427
1000Genomes African Sub 1322 G=0.5106 A=0.4894
1000Genomes East Asian Sub 1008 G=0.7669 A=0.2331
1000Genomes Europe Sub 1006 G=0.7684 A=0.2316
1000Genomes South Asian Sub 978 G=0.652 A=0.348
1000Genomes American Sub 694 G=0.624 A=0.376
Genetic variation in the Estonian population Estonian Study-wide 4480 G=0.6813 A=0.3187
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 G=0.7792 A=0.2208
UK 10K study - Twins TWIN COHORT Study-wide 3708 G=0.7832 A=0.2168
KOREAN population from KRGDB KOREAN Study-wide 2930 G=0.7672 A=0.2328
Korean Genome Project KOREAN Study-wide 1832 G=0.7609 A=0.2391
Genome of the Netherlands Release 5 Genome of the Netherlands Study-wide 998 G=0.779 A=0.221
Northern Sweden ACPOP Study-wide 600 G=0.692 A=0.308
SGDP_PRJ Global Study-wide 340 G=0.341 A=0.659
Qatari Global Study-wide 216 G=0.694 A=0.306
A Vietnamese Genetic Variation Database Global Study-wide 216 G=0.819 A=0.181
The Danish reference pan genome Danish Study-wide 40 G=0.75 A=0.25
Siberian Global Study-wide 32 G=0.47 A=0.53
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 G= A
GRCh38.p13 chr 1 NC_000001.11:g.2924348= NC_000001.11:g.2924348G>A
GRCh37.p13 chr 1 NC_000001.10:g.2840913= NC_000001.10:g.2840913G>A
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#.

47 SubSNP, 17 Frequency submissions
No Submitter Submission ID Date (Build)
1 WI_SSAHASNP ss6396343 Feb 20, 2003 (111)
2 ABI ss44041537 Mar 13, 2006 (126)
3 BGI ss105114024 Dec 01, 2009 (131)
4 ILLUMINA-UK ss118446827 Feb 14, 2009 (130)
5 ENSEMBL ss161243433 Dec 01, 2009 (131)
6 COMPLETE_GENOMICS ss162996116 Jul 04, 2010 (132)
7 BUSHMAN ss197911694 Jul 04, 2010 (132)
8 1000GENOMES ss210452713 Jul 14, 2010 (132)
9 1000GENOMES ss218198158 Jul 14, 2010 (132)
10 1000GENOMES ss230400792 Jul 14, 2010 (132)
11 1000GENOMES ss238119952 Jul 15, 2010 (132)
12 BL ss252875090 May 09, 2011 (134)
13 GMI ss275688434 May 04, 2012 (137)
14 TISHKOFF ss553726735 Apr 25, 2013 (138)
15 SSMP ss647530237 Apr 25, 2013 (138)
16 EVA-GONL ss974787187 Aug 21, 2014 (142)
17 JMKIDD_LAB ss1067621698 Aug 21, 2014 (142)
18 1000GENOMES ss1289417497 Aug 21, 2014 (142)
19 EVA_GENOME_DK ss1573857052 Apr 01, 2015 (144)
20 EVA_DECODE ss1584146695 Apr 01, 2015 (144)
21 EVA_UK10K_ALSPAC ss1599410275 Apr 01, 2015 (144)
22 EVA_UK10K_TWINSUK ss1642404308 Apr 01, 2015 (144)
23 HAMMER_LAB ss1793756018 Sep 08, 2015 (146)
24 WEILL_CORNELL_DGM ss1917982111 Feb 12, 2016 (147)
25 GENOMED ss1966669833 Jul 19, 2016 (147)
26 JJLAB ss2019507275 Sep 14, 2016 (149)
27 USC_VALOUEV ss2147497155 Dec 20, 2016 (150)
28 HUMAN_LONGEVITY ss2159504743 Dec 20, 2016 (150)
29 TOPMED ss2321660397 Dec 20, 2016 (150)
30 SYSTEMSBIOZJU ss2624269478 Nov 08, 2017 (151)
31 GRF ss2697390736 Nov 08, 2017 (151)
32 GNOMAD ss2750881106 Nov 08, 2017 (151)
33 SWEGEN ss2986187820 Nov 08, 2017 (151)
34 BIOINF_KMB_FNS_UNIBA ss3023517420 Nov 08, 2017 (151)
35 TOPMED ss3066927128 Nov 08, 2017 (151)
36 CSHL ss3343284489 Nov 08, 2017 (151)
37 EGCUT_WGS ss3654288744 Jul 12, 2019 (153)
38 EVA_DECODE ss3686030484 Jul 12, 2019 (153)
39 ACPOP ss3726732318 Jul 12, 2019 (153)
40 EVA ss3745743891 Jul 12, 2019 (153)
41 KHV_HUMAN_GENOMES ss3798766381 Jul 12, 2019 (153)
42 EVA ss3825989743 Apr 25, 2020 (154)
43 SGDP_PRJ ss3848049652 Apr 25, 2020 (154)
44 KRGDB ss3892909130 Apr 25, 2020 (154)
45 KOGIC ss3943672874 Apr 25, 2020 (154)
46 TOPMED ss4437044789 Apr 25, 2021 (155)
47 TOMMO_GENOMICS ss5142162385 Apr 25, 2021 (155)
48 1000Genomes NC_000001.10 - 2840913 Oct 11, 2018 (152)
49 The Avon Longitudinal Study of Parents and Children NC_000001.10 - 2840913 Oct 11, 2018 (152)
50 Genetic variation in the Estonian population NC_000001.10 - 2840913 Oct 11, 2018 (152)
51 The Danish reference pan genome NC_000001.10 - 2840913 Apr 25, 2020 (154)
52 gnomAD - Genomes NC_000001.11 - 2924348 Apr 25, 2021 (155)
53 Genome of the Netherlands Release 5 NC_000001.10 - 2840913 Apr 25, 2020 (154)
54 KOREAN population from KRGDB NC_000001.10 - 2840913 Apr 25, 2020 (154)
55 Korean Genome Project NC_000001.11 - 2924348 Apr 25, 2020 (154)
56 Northern Sweden NC_000001.10 - 2840913 Jul 12, 2019 (153)
57 Qatari NC_000001.10 - 2840913 Apr 25, 2020 (154)
58 SGDP_PRJ NC_000001.10 - 2840913 Apr 25, 2020 (154)
59 Siberian NC_000001.10 - 2840913 Apr 25, 2020 (154)
60 8.3KJPN NC_000001.10 - 2840913 Apr 25, 2021 (155)
61 TopMed NC_000001.11 - 2924348 Apr 25, 2021 (155)
62 UK 10K study - Twins NC_000001.10 - 2840913 Oct 11, 2018 (152)
63 A Vietnamese Genetic Variation Database NC_000001.10 - 2840913 Jul 12, 2019 (153)
64 ALFA NC_000001.11 - 2924348 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).

Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
ss118446827, ss162996116, ss197911694, ss210452713, ss252875090, ss275688434, ss1584146695 NC_000001.9:2830772:G:A NC_000001.11:2924347:G:A (self)
84536, 35198, 26992, 1364286, 14737, 86524, 17183, 24041, 66632, 13509, 131692, 35198, 7177, ss218198158, ss230400792, ss238119952, ss553726735, ss647530237, ss974787187, ss1067621698, ss1289417497, ss1573857052, ss1599410275, ss1642404308, ss1793756018, ss1917982111, ss1966669833, ss2019507275, ss2147497155, ss2321660397, ss2624269478, ss2697390736, ss2750881106, ss2986187820, ss3343284489, ss3654288744, ss3726732318, ss3745743891, ss3825989743, ss3848049652, ss3892909130, ss5142162385 NC_000001.10:2840912:G:A NC_000001.11:2924347:G:A (self)
641118, 50875, 401275, 651124, 3243438812, ss2159504743, ss3023517420, ss3066927128, ss3686030484, ss3798766381, ss3943672874, ss4437044789 NC_000001.11:2924347:G:A NC_000001.11:2924347:G:A (self)
ss6396343, ss44041537, ss105114024, ss161243433 NT_004350.19:2319544:G:A NC_000001.11:2924347:G:A (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 rs4648352

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