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dbSNP Short Genetic Variations

Examples: rs268, BRCA1 and more Advanced search

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.

rs4648348

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr1:3855711 (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
G>T
Variation Type
SNV Single Nucleotide Variation
Frequency
T=0.331048 (87625/264690, TOPMED)
T=0.330793 (46278/139900, GnomAD)
T=0.39283 (12126/30868, ALFA) (+ 15 more)
T=0.43361 (12253/28258, 14KJPN)
T=0.43693 (7323/16760, 8.3KJPN)
T=0.3076 (1970/6404, 1000G_30x)
T=0.3061 (1533/5008, 1000G)
T=0.4214 (1888/4480, Estonian)
T=0.4375 (1686/3854, ALSPAC)
T=0.4396 (1630/3708, TWINSUK)
T=0.3430 (1005/2930, KOREAN)
T=0.416 (415/998, GoNL)
T=0.442 (265/600, NorthernSweden)
G=0.372 (110/296, SGDP_PRJ)
T=0.255 (55/216, Qatari)
T=0.278 (59/212, Vietnamese)
T=0.35 (14/40, GENOME_DK)
G=0.40 (12/30, Siberian)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
CEP104 : Intron Variant
DFFB : 2KB Upstream 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 30868 G=0.60717 T=0.39283
European Sub 24738 G=0.56929 T=0.43071
African Sub 3168 G=0.8772 T=0.1228
African Others Sub 124 G=0.944 T=0.056
African American Sub 3044 G=0.8745 T=0.1255
Asian Sub 128 G=0.672 T=0.328
East Asian Sub 100 G=0.72 T=0.28
Other Asian Sub 28 G=0.50 T=0.50
Latin American 1 Sub 168 G=0.685 T=0.315
Latin American 2 Sub 700 G=0.587 T=0.413
South Asian Sub 114 G=0.754 T=0.246
Other Sub 1852 G=0.6382 T=0.3618


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=0.668952 T=0.331048
gnomAD - Genomes Global Study-wide 139900 G=0.669207 T=0.330793
gnomAD - Genomes European Sub 75734 G=0.58204 T=0.41796
gnomAD - Genomes African Sub 41952 G=0.86742 T=0.13258
gnomAD - Genomes American Sub 13634 G=0.54870 T=0.45130
gnomAD - Genomes Ashkenazi Jewish Sub 3320 G=0.6524 T=0.3476
gnomAD - Genomes East Asian Sub 3112 G=0.6806 T=0.3194
gnomAD - Genomes Other Sub 2148 G=0.6457 T=0.3543
Allele Frequency Aggregator Total Global 30868 G=0.60717 T=0.39283
Allele Frequency Aggregator European Sub 24738 G=0.56929 T=0.43071
Allele Frequency Aggregator African Sub 3168 G=0.8772 T=0.1228
Allele Frequency Aggregator Other Sub 1852 G=0.6382 T=0.3618
Allele Frequency Aggregator Latin American 2 Sub 700 G=0.587 T=0.413
Allele Frequency Aggregator Latin American 1 Sub 168 G=0.685 T=0.315
Allele Frequency Aggregator Asian Sub 128 G=0.672 T=0.328
Allele Frequency Aggregator South Asian Sub 114 G=0.754 T=0.246
14KJPN JAPANESE Study-wide 28258 G=0.56639 T=0.43361
8.3KJPN JAPANESE Study-wide 16760 G=0.56307 T=0.43693
1000Genomes_30x Global Study-wide 6404 G=0.6924 T=0.3076
1000Genomes_30x African Sub 1786 G=0.9272 T=0.0728
1000Genomes_30x Europe Sub 1266 G=0.5687 T=0.4313
1000Genomes_30x South Asian Sub 1202 G=0.6714 T=0.3286
1000Genomes_30x East Asian Sub 1170 G=0.6590 T=0.3410
1000Genomes_30x American Sub 980 G=0.490 T=0.510
1000Genomes Global Study-wide 5008 G=0.6939 T=0.3061
1000Genomes African Sub 1322 G=0.9228 T=0.0772
1000Genomes East Asian Sub 1008 G=0.6627 T=0.3373
1000Genomes Europe Sub 1006 G=0.5716 T=0.4284
1000Genomes South Asian Sub 978 G=0.673 T=0.327
1000Genomes American Sub 694 G=0.510 T=0.490
Genetic variation in the Estonian population Estonian Study-wide 4480 G=0.5786 T=0.4214
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 G=0.5625 T=0.4375
UK 10K study - Twins TWIN COHORT Study-wide 3708 G=0.5604 T=0.4396
KOREAN population from KRGDB KOREAN Study-wide 2930 G=0.6570 T=0.3430
Genome of the Netherlands Release 5 Genome of the Netherlands Study-wide 998 G=0.584 T=0.416
Northern Sweden ACPOP Study-wide 600 G=0.558 T=0.442
SGDP_PRJ Global Study-wide 296 G=0.372 T=0.628
Qatari Global Study-wide 216 G=0.745 T=0.255
A Vietnamese Genetic Variation Database Global Study-wide 212 G=0.722 T=0.278
The Danish reference pan genome Danish Study-wide 40 G=0.65 T=0.35
Siberian Global Study-wide 30 G=0.40 T=0.60
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.p14 chr 1 NC_000001.11:g.3855711G>T
GRCh37.p13 chr 1 NC_000001.10:g.3772275G>T
CEP104 RefSeqGene NG_046726.1:g.6523C>A
Gene: CEP104, centrosomal protein 104 (minus strand)
Molecule type Change Amino acid[Codon] SO Term
CEP104 transcript NM_014704.4:c.-15+1178C>A N/A Intron Variant
CEP104 transcript variant X2 XM_005244815.5:c.94+163C>A N/A Intron Variant
CEP104 transcript variant X1 XM_024451101.2:c.94+163C>A N/A Intron Variant
CEP104 transcript variant X3 XM_024451102.2:c.94+163C>A N/A Intron Variant
CEP104 transcript variant X5 XM_024451104.2:c.94+163C>A N/A Intron Variant
CEP104 transcript variant X7 XM_024451106.2:c.94+163C>A N/A Intron Variant
CEP104 transcript variant X8 XM_024451108.2:c.94+163C>A N/A Intron Variant
CEP104 transcript variant X4 XM_047435158.1:c.94+163C>A N/A Intron Variant
CEP104 transcript variant X6 XM_047435161.1:c.94+163C>A N/A Intron Variant
Gene: DFFB, DNA fragmentation factor subunit beta (plus strand) : 2KB Upstream Variant
Molecule type Change Amino acid[Codon] SO Term
DFFB transcript variant 1 NM_001282669.2:c. N/A Upstream Transcript Variant
DFFB transcript variant 4 NM_001320132.2:c. N/A Upstream Transcript Variant
DFFB transcript variant 5 NM_001320136.2:c. N/A Upstream Transcript Variant
DFFB transcript variant 2 NM_004402.4:c. N/A Upstream Transcript Variant
DFFB transcript variant 3 NR_104222.2:n. N/A Upstream Transcript Variant
DFFB transcript variant 6 NR_135150.2:n. N/A Upstream Transcript Variant
DFFB transcript variant 7 NR_135151.2:n. N/A Upstream Transcript Variant
DFFB transcript variant 8 NR_135152.2:n. N/A Upstream Transcript Variant
DFFB transcript variant X7 XM_011540865.3:c. N/A Upstream Transcript Variant
DFFB transcript variant X3 XM_017000498.3:c. N/A Upstream Transcript Variant
DFFB transcript variant X4 XM_017000499.2:c. N/A Upstream Transcript Variant
DFFB transcript variant X6 XM_017000500.2:c. N/A Upstream Transcript Variant
DFFB transcript variant X2 XR_002959574.2:n. N/A Upstream Transcript Variant
DFFB transcript variant X1 XR_946563.3:n. N/A Upstream Transcript Variant
DFFB transcript variant X5 XR_946565.2:n. N/A Upstream Transcript 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
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= T
GRCh38.p14 chr 1 NC_000001.11:g.3855711= NC_000001.11:g.3855711G>T
GRCh37.p13 chr 1 NC_000001.10:g.3772275= NC_000001.10:g.3772275G>T
CEP104 RefSeqGene NG_046726.1:g.6523= NG_046726.1:g.6523C>A
CEP104 transcript NM_014704.3:c.-15+1178= NM_014704.3:c.-15+1178C>A
CEP104 transcript NM_014704.4:c.-15+1178= NM_014704.4:c.-15+1178C>A
CEP104 transcript variant X1 XM_005244815.1:c.94+163= XM_005244815.1:c.94+163C>A
CEP104 transcript variant X2 XM_005244815.5:c.94+163= XM_005244815.5:c.94+163C>A
CEP104 transcript variant X1 XM_024451101.2:c.94+163= XM_024451101.2:c.94+163C>A
CEP104 transcript variant X3 XM_024451102.2:c.94+163= XM_024451102.2:c.94+163C>A
CEP104 transcript variant X5 XM_024451104.2:c.94+163= XM_024451104.2:c.94+163C>A
CEP104 transcript variant X7 XM_024451106.2:c.94+163= XM_024451106.2:c.94+163C>A
CEP104 transcript variant X8 XM_024451108.2:c.94+163= XM_024451108.2:c.94+163C>A
CEP104 transcript variant X4 XM_047435158.1:c.94+163= XM_047435158.1:c.94+163C>A
CEP104 transcript variant X6 XM_047435161.1:c.94+163= XM_047435161.1:c.94+163C>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#.

72 SubSNP, 18 Frequency submissions
No Submitter Submission ID Date (Build)
1 WI_SSAHASNP ss6396337 Feb 20, 2003 (111)
2 HGSV ss81630999 Dec 14, 2007 (130)
3 BCMHGSC_JDW ss87174968 Mar 23, 2008 (129)
4 1000GENOMES ss107949466 Jan 22, 2009 (130)
5 ILLUMINA-UK ss118453960 Feb 14, 2009 (130)
6 ENSEMBL ss137763931 Dec 01, 2009 (131)
7 GMI ss154560245 Dec 01, 2009 (131)
8 COMPLETE_GENOMICS ss166009664 Jul 04, 2010 (132)
9 1000GENOMES ss218203554 Jul 14, 2010 (132)
10 1000GENOMES ss230404384 Jul 14, 2010 (132)
11 1000GENOMES ss238123221 Jul 15, 2010 (132)
12 GMI ss275691658 May 04, 2012 (137)
13 GMI ss283991124 Apr 25, 2013 (138)
14 PJP ss290498464 May 09, 2011 (134)
15 ILLUMINA ss479550824 May 04, 2012 (137)
16 ILLUMINA ss482327748 May 04, 2012 (137)
17 ILLUMINA ss533082083 Sep 08, 2015 (146)
18 TISHKOFF ss553734977 Apr 25, 2013 (138)
19 SSMP ss647536824 Apr 25, 2013 (138)
20 ILLUMINA ss779607698 Sep 08, 2015 (146)
21 ILLUMINA ss781009516 Sep 08, 2015 (146)
22 ILLUMINA ss835079835 Sep 08, 2015 (146)
23 EVA-GONL ss974796946 Aug 21, 2014 (142)
24 JMKIDD_LAB ss1067627696 Aug 21, 2014 (142)
25 1000GENOMES ss1289453254 Aug 21, 2014 (142)
26 DDI ss1425693265 Apr 01, 2015 (144)
27 EVA_GENOME_DK ss1573860402 Apr 01, 2015 (144)
28 EVA_DECODE ss1584155691 Apr 01, 2015 (144)
29 EVA_UK10K_ALSPAC ss1599428177 Apr 01, 2015 (144)
30 EVA_UK10K_TWINSUK ss1642422210 Apr 01, 2015 (144)
31 WEILL_CORNELL_DGM ss1917992476 Feb 12, 2016 (147)
32 GENOMED ss1966671528 Jul 19, 2016 (147)
33 JJLAB ss2019512477 Sep 14, 2016 (149)
34 USC_VALOUEV ss2147502812 Dec 20, 2016 (150)
35 HUMAN_LONGEVITY ss2159577558 Dec 20, 2016 (150)
36 SYSTEMSBIOZJU ss2624272016 Nov 08, 2017 (151)
37 ILLUMINA ss2632468738 Nov 08, 2017 (151)
38 GRF ss2697396897 Nov 08, 2017 (151)
39 GNOMAD ss2750976220 Nov 08, 2017 (151)
40 SWEGEN ss2986202001 Nov 08, 2017 (151)
41 BIOINF_KMB_FNS_UNIBA ss3023519893 Nov 08, 2017 (151)
42 CSHL ss3343289249 Nov 08, 2017 (151)
43 ILLUMINA ss3626012060 Oct 11, 2018 (152)
44 ILLUMINA ss3630508039 Oct 11, 2018 (152)
45 ILLUMINA ss3641567892 Oct 11, 2018 (152)
46 EGCUT_WGS ss3654303190 Jul 12, 2019 (153)
47 EVA_DECODE ss3686048054 Jul 12, 2019 (153)
48 ACPOP ss3726740474 Jul 12, 2019 (153)
49 EVA ss3745755938 Jul 12, 2019 (153)
50 KHV_HUMAN_GENOMES ss3798777607 Jul 12, 2019 (153)
51 EVA ss3825994264 Apr 25, 2020 (154)
52 EVA ss3836384334 Apr 25, 2020 (154)
53 EVA ss3841788514 Apr 25, 2020 (154)
54 SGDP_PRJ ss3848070367 Apr 25, 2020 (154)
55 KRGDB ss3892932067 Apr 25, 2020 (154)
56 TOPMED ss4437316363 Apr 25, 2021 (155)
57 TOMMO_GENOMICS ss5142203362 Apr 25, 2021 (155)
58 1000G_HIGH_COVERAGE ss5240969614 Oct 13, 2022 (156)
59 EVA ss5314587813 Oct 13, 2022 (156)
60 EVA ss5316376042 Oct 13, 2022 (156)
61 HUGCELL_USP ss5442195087 Oct 13, 2022 (156)
62 EVA ss5505751865 Oct 13, 2022 (156)
63 1000G_HIGH_COVERAGE ss5512635873 Oct 13, 2022 (156)
64 SANFORD_IMAGENETICS ss5624809440 Oct 13, 2022 (156)
65 TOMMO_GENOMICS ss5666417563 Oct 13, 2022 (156)
66 EVA ss5800077123 Oct 13, 2022 (156)
67 YY_MCH ss5800272031 Oct 13, 2022 (156)
68 EVA ss5831460311 Oct 13, 2022 (156)
69 EVA ss5848759422 Oct 13, 2022 (156)
70 EVA ss5906812509 Oct 13, 2022 (156)
71 EVA ss5936634201 Oct 13, 2022 (156)
72 EVA ss5979928825 Oct 13, 2022 (156)
73 1000Genomes NC_000001.10 - 3772275 Oct 11, 2018 (152)
74 1000Genomes_30x NC_000001.11 - 3855711 Oct 13, 2022 (156)
75 The Avon Longitudinal Study of Parents and Children NC_000001.10 - 3772275 Oct 11, 2018 (152)
76 Genetic variation in the Estonian population NC_000001.10 - 3772275 Oct 11, 2018 (152)
77 The Danish reference pan genome NC_000001.10 - 3772275 Apr 25, 2020 (154)
78 gnomAD - Genomes NC_000001.11 - 3855711 Apr 25, 2021 (155)
79 Genome of the Netherlands Release 5 NC_000001.10 - 3772275 Apr 25, 2020 (154)
80 KOREAN population from KRGDB NC_000001.10 - 3772275 Apr 25, 2020 (154)
81 Northern Sweden NC_000001.10 - 3772275 Jul 12, 2019 (153)
82 Qatari NC_000001.10 - 3772275 Apr 25, 2020 (154)
83 SGDP_PRJ NC_000001.10 - 3772275 Apr 25, 2020 (154)
84 Siberian NC_000001.10 - 3772275 Apr 25, 2020 (154)
85 8.3KJPN NC_000001.10 - 3772275 Apr 25, 2021 (155)
86 14KJPN NC_000001.11 - 3855711 Oct 13, 2022 (156)
87 TopMed NC_000001.11 - 3855711 Apr 25, 2021 (155)
88 UK 10K study - Twins NC_000001.10 - 3772275 Oct 11, 2018 (152)
89 A Vietnamese Genetic Variation Database NC_000001.10 - 3772275 Jul 12, 2019 (153)
90 ALFA NC_000001.11 - 3855711 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)
rs57589760 May 23, 2008 (130)
Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
ss81630999 NC_000001.8:3795431:G:T NC_000001.11:3855710:G:T (self)
ss87174968, ss107949466, ss118453960, ss166009664, ss275691658, ss283991124, ss290498464, ss482327748, ss1584155691 NC_000001.9:3762134:G:T NC_000001.11:3855710:G:T (self)
121338, 54503, 41438, 1367636, 23549, 109461, 25339, 34406, 87347, 19166, 172669, 54503, 11585, ss218203554, ss230404384, ss238123221, ss479550824, ss533082083, ss553734977, ss647536824, ss779607698, ss781009516, ss835079835, ss974796946, ss1067627696, ss1289453254, ss1425693265, ss1573860402, ss1599428177, ss1642422210, ss1917992476, ss1966671528, ss2019512477, ss2147502812, ss2624272016, ss2632468738, ss2697396897, ss2750976220, ss2986202001, ss3343289249, ss3626012060, ss3630508039, ss3641567892, ss3654303190, ss3726740474, ss3745755938, ss3825994264, ss3836384334, ss3848070367, ss3892932067, ss5142203362, ss5314587813, ss5316376042, ss5505751865, ss5624809440, ss5800077123, ss5831460311, ss5936634201, ss5979928825 NC_000001.10:3772274:G:T NC_000001.11:3855710:G:T (self)
161808, 872742, 254667, 922698, 2939168860, ss2159577558, ss3023519893, ss3686048054, ss3798777607, ss3841788514, ss4437316363, ss5240969614, ss5442195087, ss5512635873, ss5666417563, ss5800272031, ss5848759422, ss5906812509 NC_000001.11:3855710:G:T NC_000001.11:3855710:G:T (self)
ss6396337, ss137763931, ss154560245 NT_004350.19:3250906:G:T NC_000001.11:3855710:G: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 rs4648348

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.post761+d5e8e07