Skip to main page content
Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation

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.

rs4648349

Current Build 155

Released April 9, 2021

Organism
Homo sapiens
Position
chr1:3856375 (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 / G>C
Variation Type
SNV Single Nucleotide Variation
Frequency
C=0.380838 (100804/264690, TOPMED)
C=0.377167 (52832/140076, GnomAD)
C=0.17900 (3000/16760, 8.3KJPN) (+ 13 more)
C=0.15613 (1867/11958, ALFA)
C=0.3648 (1827/5008, 1000G)
C=0.2560 (1147/4480, Estonian)
C=0.2582 (995/3854, ALSPAC)
C=0.2673 (991/3708, TWINSUK)
C=0.1762 (515/2922, KOREAN)
C=0.282 (281/998, GoNL)
C=0.317 (190/600, NorthernSweden)
G=0.381 (96/252, SGDP_PRJ)
C=0.463 (100/216, Qatari)
C=0.126 (27/214, Vietnamese)
C=0.35 (14/40, GENOME_DK)
G=0.33 (4/12, 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
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.3856375G>A
GRCh38.p13 chr 1 NC_000001.11:g.3856375G>C
GRCh37.p13 chr 1 NC_000001.10:g.3772939G>A
GRCh37.p13 chr 1 NC_000001.10:g.3772939G>C
CEP104 RefSeqGene NG_046726.1:g.5859C>T
CEP104 RefSeqGene NG_046726.1:g.5859C>G
Gene: CEP104, centrosomal protein 104 (minus strand)
Molecule type Change Amino acid[Codon] SO Term
CEP104 transcript NM_014704.4:c.-15+514C>T N/A Intron Variant
CEP104 transcript variant X2 XM_005244815.4:c.-34-374C…

XM_005244815.4:c.-34-374C>T

N/A Intron Variant
CEP104 transcript variant X3 XM_011542474.3:c.-15+514C…

XM_011542474.3:c.-15+514C>T

N/A Intron Variant
CEP104 transcript variant X7 XM_017002918.2:c.-15+514C…

XM_017002918.2:c.-15+514C>T

N/A Intron Variant
CEP104 transcript variant X8 XM_017002919.2:c.-15+514C…

XM_017002919.2:c.-15+514C>T

N/A Intron Variant
CEP104 transcript variant X1 XM_024451101.1:c. N/A Genic Upstream Transcript Variant
CEP104 transcript variant X4 XM_024451102.1:c. N/A Genic Upstream Transcript Variant
CEP104 transcript variant X5 XM_024451103.1:c. N/A Genic Upstream Transcript Variant
CEP104 transcript variant X6 XM_024451104.1:c. N/A Genic Upstream Transcript Variant
CEP104 transcript variant X9 XM_024451106.1:c. N/A Genic Upstream Transcript Variant
CEP104 transcript variant X10 XM_024451108.1:c. N/A Genic Upstream Transcript 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 X10 XM_011540865.2:c. N/A Upstream Transcript Variant
DFFB transcript variant X6 XM_017000498.2:c. N/A Upstream Transcript Variant
DFFB transcript variant X7 XM_017000499.1:c. N/A Upstream Transcript Variant
DFFB transcript variant X9 XM_017000500.1:c. N/A Upstream Transcript Variant
DFFB transcript variant X5 XR_001737013.1:n. N/A Upstream Transcript Variant
DFFB transcript variant X4 XR_002959574.1:n. N/A Upstream Transcript Variant
DFFB transcript variant X1 XR_946563.2:n. N/A Upstream Transcript Variant
DFFB transcript variant X8 XR_946565.1:n. N/A Upstream Transcript Variant
DFFB transcript variant X2 XR_001737011.2:n. N/A N/A
DFFB transcript variant X3 XR_001737012.2:n. N/A N/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 11958 G=0.84387 A=0.00000, C=0.15613
European Sub 10566 G=0.83778 A=0.00000, C=0.16222
African Sub 494 G=0.844 A=0.000, C=0.156
African Others Sub 16 G=0.62 A=0.00, C=0.38
African American Sub 478 G=0.851 A=0.000, C=0.149
Asian Sub 70 G=1.00 A=0.00, C=0.00
East Asian Sub 48 G=1.00 A=0.00, C=0.00
Other Asian Sub 22 G=1.00 A=0.00, C=0.00
Latin American 1 Sub 58 G=1.00 A=0.00, C=0.00
Latin American 2 Sub 328 G=1.000 A=0.000, C=0.000
South Asian Sub 42 G=0.95 A=0.00, C=0.05
Other Sub 400 G=0.815 A=0.000, C=0.185


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=0.619162 C=0.380838
gnomAD - Genomes Global Study-wide 140076 G=0.622833 C=0.377167
gnomAD - Genomes European Sub 75858 G=0.73226 C=0.26774
gnomAD - Genomes African Sub 41968 G=0.36735 C=0.63265
gnomAD - Genomes American Sub 13644 G=0.73593 C=0.26407
gnomAD - Genomes Ashkenazi Jewish Sub 3322 G=0.6629 C=0.3371
gnomAD - Genomes East Asian Sub 3130 G=0.8412 C=0.1588
gnomAD - Genomes Other Sub 2154 G=0.6513 C=0.3487
8.3KJPN JAPANESE Study-wide 16760 G=0.82100 C=0.17900
1000Genomes Global Study-wide 5008 G=0.6352 C=0.3648
1000Genomes African Sub 1322 G=0.2935 C=0.7065
1000Genomes East Asian Sub 1008 G=0.8492 C=0.1508
1000Genomes Europe Sub 1006 G=0.6978 C=0.3022
1000Genomes South Asian Sub 978 G=0.720 C=0.280
1000Genomes American Sub 694 G=0.765 C=0.235
Genetic variation in the Estonian population Estonian Study-wide 4480 G=0.7440 C=0.2560
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 G=0.7418 C=0.2582
UK 10K study - Twins TWIN COHORT Study-wide 3708 G=0.7327 C=0.2673
KOREAN population from KRGDB KOREAN Study-wide 2922 G=0.8238 C=0.1762
Genome of the Netherlands Release 5 Genome of the Netherlands Study-wide 998 G=0.718 C=0.282
Northern Sweden ACPOP Study-wide 600 G=0.683 C=0.317
SGDP_PRJ Global Study-wide 252 G=0.381 C=0.619
Qatari Global Study-wide 216 G=0.537 C=0.463
A Vietnamese Genetic Variation Database Global Study-wide 214 G=0.874 C=0.126
The Danish reference pan genome Danish Study-wide 40 G=0.65 C=0.35
Siberian Global Study-wide 12 G=0.33 C=0.67
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 C
GRCh38.p13 chr 1 NC_000001.11:g.3856375= NC_000001.11:g.3856375G>A NC_000001.11:g.3856375G>C
GRCh37.p13 chr 1 NC_000001.10:g.3772939= NC_000001.10:g.3772939G>A NC_000001.10:g.3772939G>C
CEP104 RefSeqGene NG_046726.1:g.5859= NG_046726.1:g.5859C>T NG_046726.1:g.5859C>G
CEP104 transcript NM_014704.3:c.-15+514= NM_014704.3:c.-15+514C>T NM_014704.3:c.-15+514C>G
CEP104 transcript NM_014704.4:c.-15+514= NM_014704.4:c.-15+514C>T NM_014704.4:c.-15+514C>G
CEP104 transcript variant X2 XM_005244815.4:c.-34-374= XM_005244815.4:c.-34-374C>T XM_005244815.4:c.-34-374C>G
CEP104 transcript variant X3 XM_011542474.3:c.-15+514= XM_011542474.3:c.-15+514C>T XM_011542474.3:c.-15+514C>G
CEP104 transcript variant X7 XM_017002918.2:c.-15+514= XM_017002918.2:c.-15+514C>T XM_017002918.2:c.-15+514C>G
CEP104 transcript variant X8 XM_017002919.2:c.-15+514= XM_017002919.2:c.-15+514C>T XM_017002919.2:c.-15+514C>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#.

59 SubSNP, 16 Frequency submissions
No Submitter Submission ID Date (Build)
1 WI_SSAHASNP ss6396338 Feb 20, 2003 (111)
2 SSAHASNP ss20604824 Apr 05, 2004 (121)
3 HGSV ss77439695 Dec 07, 2007 (129)
4 HGSV ss83398886 Dec 15, 2007 (130)
5 HGSV ss85418254 Dec 15, 2007 (130)
6 HUMANGENOME_JCVI ss97915581 Feb 05, 2009 (130)
7 1000GENOMES ss109968532 Jan 24, 2009 (130)
8 ILLUMINA-UK ss118453968 Dec 01, 2009 (131)
9 ENSEMBL ss144020685 Dec 01, 2009 (131)
10 COMPLETE_GENOMICS ss163005619 Jul 04, 2010 (132)
11 COMPLETE_GENOMICS ss163739661 Jul 04, 2010 (132)
12 BUSHMAN ss197925944 Jul 04, 2010 (132)
13 BCM-HGSC-SUB ss205390968 Jul 04, 2010 (132)
14 1000GENOMES ss218203556 Jul 14, 2010 (132)
15 1000GENOMES ss230404387 Jul 14, 2010 (132)
16 1000GENOMES ss238123223 Jul 15, 2010 (132)
17 BL ss252880996 May 09, 2011 (134)
18 GMI ss275691660 May 04, 2012 (137)
19 PJP ss290498466 May 09, 2011 (134)
20 TISHKOFF ss553734980 Apr 25, 2013 (138)
21 SSMP ss647536830 Apr 25, 2013 (138)
22 EVA-GONL ss974796951 Aug 21, 2014 (142)
23 JMKIDD_LAB ss1067627700 Aug 21, 2014 (142)
24 1000GENOMES ss1289453275 Aug 21, 2014 (142)
25 DDI ss1425693268 Apr 01, 2015 (144)
26 EVA_GENOME_DK ss1573860406 Apr 01, 2015 (144)
27 EVA_DECODE ss1584155695 Apr 01, 2015 (144)
28 EVA_UK10K_ALSPAC ss1599428188 Apr 01, 2015 (144)
29 EVA_UK10K_TWINSUK ss1642422221 Apr 01, 2015 (144)
30 HAMMER_LAB ss1793785889 Sep 08, 2015 (146)
31 WEILL_CORNELL_DGM ss1917992481 Feb 12, 2016 (147)
32 JJLAB ss2019512481 Sep 14, 2016 (149)
33 USC_VALOUEV ss2147502816 Dec 20, 2016 (150)
34 HUMAN_LONGEVITY ss2159577596 Dec 20, 2016 (150)
35 TOPMED ss2321732483 Dec 20, 2016 (150)
36 SYSTEMSBIOZJU ss2624272018 Nov 08, 2017 (151)
37 GRF ss2697396900 Nov 08, 2017 (151)
38 GNOMAD ss2750976275 Nov 08, 2017 (151)
39 SWEGEN ss2986202008 Nov 08, 2017 (151)
40 BIOINF_KMB_FNS_UNIBA ss3023519897 Nov 08, 2017 (151)
41 TOPMED ss3067135042 Nov 08, 2017 (151)
42 TOPMED ss3067135043 Nov 08, 2017 (151)
43 CSHL ss3343289253 Nov 08, 2017 (151)
44 URBANLAB ss3646586909 Oct 11, 2018 (152)
45 EGCUT_WGS ss3654303198 Jul 12, 2019 (153)
46 EVA_DECODE ss3686048059 Jul 12, 2019 (153)
47 ACPOP ss3726740480 Jul 12, 2019 (153)
48 EVA ss3745755944 Jul 12, 2019 (153)
49 PACBIO ss3783308943 Jul 12, 2019 (153)
50 PACBIO ss3788985823 Jul 12, 2019 (153)
51 PACBIO ss3793858449 Jul 12, 2019 (153)
52 KHV_HUMAN_GENOMES ss3798777612 Jul 12, 2019 (153)
53 EVA ss3825994267 Apr 25, 2020 (154)
54 EVA ss3836384336 Apr 25, 2020 (154)
55 EVA ss3841788516 Apr 25, 2020 (154)
56 SGDP_PRJ ss3848070375 Apr 25, 2020 (154)
57 KRGDB ss3892932072 Apr 25, 2020 (154)
58 TOPMED ss4437316535 Apr 25, 2021 (155)
59 TOMMO_GENOMICS ss5142203376 Apr 25, 2021 (155)
60 1000Genomes NC_000001.10 - 3772939 Oct 11, 2018 (152)
61 The Avon Longitudinal Study of Parents and Children NC_000001.10 - 3772939 Oct 11, 2018 (152)
62 Genetic variation in the Estonian population NC_000001.10 - 3772939 Oct 11, 2018 (152)
63 The Danish reference pan genome NC_000001.10 - 3772939 Apr 25, 2020 (154)
64 gnomAD - Genomes NC_000001.11 - 3856375 Apr 25, 2021 (155)
65 Genome of the Netherlands Release 5 NC_000001.10 - 3772939 Apr 25, 2020 (154)
66 KOREAN population from KRGDB NC_000001.10 - 3772939 Apr 25, 2020 (154)
67 Northern Sweden NC_000001.10 - 3772939 Jul 12, 2019 (153)
68 Qatari NC_000001.10 - 3772939 Apr 25, 2020 (154)
69 SGDP_PRJ NC_000001.10 - 3772939 Apr 25, 2020 (154)
70 Siberian NC_000001.10 - 3772939 Apr 25, 2020 (154)
71 8.3KJPN NC_000001.10 - 3772939 Apr 25, 2021 (155)
72 TopMed NC_000001.11 - 3856375 Apr 25, 2021 (155)
73 UK 10K study - Twins NC_000001.10 - 3772939 Oct 11, 2018 (152)
74 A Vietnamese Genetic Variation Database NC_000001.10 - 3772939 Jul 12, 2019 (153)
75 ALFA NC_000001.11 - 3856375 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)
rs59080939 May 25, 2008 (130)
Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
14526451970, ss3067135042 NC_000001.11:3856374:G:A NC_000001.11:3856374:G:A (self)
ss77439695, ss83398886, ss85418254 NC_000001.8:3796095:G:C NC_000001.11:3856374:G:C (self)
ss109968532, ss118453968, ss163005619, ss163739661, ss197925944, ss205390968, ss252880996, ss275691660, ss290498466, ss1584155695 NC_000001.9:3762798:G:C NC_000001.11:3856374:G:C (self)
121359, 54515, 41446, 1367640, 23554, 109466, 25345, 34411, 87355, 19170, 172683, 54515, 11588, ss218203556, ss230404387, ss238123223, ss553734980, ss647536830, ss974796951, ss1067627700, ss1289453275, ss1425693268, ss1573860406, ss1599428188, ss1642422221, ss1793785889, ss1917992481, ss2019512481, ss2147502816, ss2321732483, ss2624272018, ss2697396900, ss2750976275, ss2986202008, ss3343289253, ss3654303198, ss3726740480, ss3745755944, ss3783308943, ss3788985823, ss3793858449, ss3825994267, ss3836384336, ss3848070375, ss3892932072, ss5142203376 NC_000001.10:3772938:G:C NC_000001.11:3856374:G:C (self)
872869, 574747, 922870, 14526451970, ss2159577596, ss3023519897, ss3067135043, ss3646586909, ss3686048059, ss3798777612, ss3841788516, ss4437316535 NC_000001.11:3856374:G:C NC_000001.11:3856374:G:C (self)
ss20604824 NT_004321.15:1079712:G:C NC_000001.11:3856374:G:C (self)
ss6396338, ss97915581, ss144020685 NT_004350.19:3251570:G:C NC_000001.11:3856374:G:C (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 rs4648349

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