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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.

rs34085539

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr4:17804008 (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>C
Variation Type
SNV Single Nucleotide Variation
Frequency
C=0.018248 (4830/264690, TOPMED)
C=0.004101 (1031/251430, GnomAD_exome)
C=0.002545 (553/217294, ALFA) (+ 9 more)
C=0.017694 (2481/140218, GnomAD)
C=0.005167 (626/121144, ExAC)
C=0.02633 (2072/78700, PAGE_STUDY)
C=0.02084 (271/13006, GO-ESP)
C=0.0178 (114/6404, 1000G_30x)
C=0.0154 (77/5008, 1000G)
C=0.009 (2/216, Qatari)
T=0.5 (3/6, SGDP_PRJ)
C=0.5 (3/6, SGDP_PRJ)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
DCAF16 : Missense 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 233690 T=0.996341 C=0.003659
European Sub 191770 T=0.999880 C=0.000120
African Sub 12954 T=0.94017 C=0.05983
African Others Sub 452 T=0.929 C=0.071
African American Sub 12502 T=0.94057 C=0.05943
Asian Sub 6388 T=1.0000 C=0.0000
East Asian Sub 4534 T=1.0000 C=0.0000
Other Asian Sub 1854 T=1.0000 C=0.0000
Latin American 1 Sub 834 T=0.987 C=0.013
Latin American 2 Sub 1092 T=0.9973 C=0.0027
South Asian Sub 312 T=1.000 C=0.000
Other Sub 20340 T=0.99789 C=0.00211


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=0.981752 C=0.018248
gnomAD - Exomes Global Study-wide 251430 T=0.995899 C=0.004101
gnomAD - Exomes European Sub 135366 T=0.999919 C=0.000081
gnomAD - Exomes Asian Sub 49008 T=0.99996 C=0.00004
gnomAD - Exomes American Sub 34588 T=0.99769 C=0.00231
gnomAD - Exomes African Sub 16248 T=0.94245 C=0.05755
gnomAD - Exomes Ashkenazi Jewish Sub 10080 T=1.00000 C=0.00000
gnomAD - Exomes Other Sub 6140 T=0.9995 C=0.0005
Allele Frequency Aggregator Total Global 217294 T=0.997455 C=0.002545
Allele Frequency Aggregator European Sub 181636 T=0.999895 C=0.000105
Allele Frequency Aggregator Other Sub 18908 T=0.99836 C=0.00164
Allele Frequency Aggregator African Sub 8124 T=0.9398 C=0.0602
Allele Frequency Aggregator Asian Sub 6388 T=1.0000 C=0.0000
Allele Frequency Aggregator Latin American 2 Sub 1092 T=0.9973 C=0.0027
Allele Frequency Aggregator Latin American 1 Sub 834 T=0.987 C=0.013
Allele Frequency Aggregator South Asian Sub 312 T=1.000 C=0.000
gnomAD - Genomes Global Study-wide 140218 T=0.982306 C=0.017694
gnomAD - Genomes European Sub 75954 T=0.99987 C=0.00013
gnomAD - Genomes African Sub 42012 T=0.94314 C=0.05686
gnomAD - Genomes American Sub 13644 T=0.99575 C=0.00425
gnomAD - Genomes Ashkenazi Jewish Sub 3322 T=1.0000 C=0.0000
gnomAD - Genomes East Asian Sub 3134 T=1.0000 C=0.0000
gnomAD - Genomes Other Sub 2152 T=0.9888 C=0.0112
ExAC Global Study-wide 121144 T=0.994833 C=0.005167
ExAC Europe Sub 73220 T=0.99997 C=0.00003
ExAC Asian Sub 25140 T=0.99992 C=0.00008
ExAC American Sub 11554 T=0.99775 C=0.00225
ExAC African Sub 10324 T=0.94227 C=0.05773
ExAC Other Sub 906 T=1.000 C=0.000
The PAGE Study Global Study-wide 78700 T=0.97367 C=0.02633
The PAGE Study AfricanAmerican Sub 32516 T=0.94529 C=0.05471
The PAGE Study Mexican Sub 10810 T=0.99769 C=0.00231
The PAGE Study Asian Sub 8318 T=1.0000 C=0.0000
The PAGE Study PuertoRican Sub 7916 T=0.9879 C=0.0121
The PAGE Study NativeHawaiian Sub 4534 T=0.9998 C=0.0002
The PAGE Study Cuban Sub 4230 T=0.9927 C=0.0073
The PAGE Study Dominican Sub 3828 T=0.9739 C=0.0261
The PAGE Study CentralAmerican Sub 2450 T=0.9931 C=0.0069
The PAGE Study SouthAmerican Sub 1982 T=0.9960 C=0.0040
The PAGE Study NativeAmerican Sub 1260 T=0.9881 C=0.0119
The PAGE Study SouthAsian Sub 856 T=1.000 C=0.000
GO Exome Sequencing Project Global Study-wide 13006 T=0.97916 C=0.02084
GO Exome Sequencing Project European American Sub 8600 T=0.9999 C=0.0001
GO Exome Sequencing Project African American Sub 4406 T=0.9387 C=0.0613
1000Genomes_30x Global Study-wide 6404 T=0.9822 C=0.0178
1000Genomes_30x African Sub 1786 T=0.9406 C=0.0594
1000Genomes_30x Europe Sub 1266 T=1.0000 C=0.0000
1000Genomes_30x South Asian Sub 1202 T=1.0000 C=0.0000
1000Genomes_30x East Asian Sub 1170 T=1.0000 C=0.0000
1000Genomes_30x American Sub 980 T=0.992 C=0.008
1000Genomes Global Study-wide 5008 T=0.9846 C=0.0154
1000Genomes African Sub 1322 T=0.9463 C=0.0537
1000Genomes East Asian Sub 1008 T=1.0000 C=0.0000
1000Genomes Europe Sub 1006 T=1.0000 C=0.0000
1000Genomes South Asian Sub 978 T=1.000 C=0.000
1000Genomes American Sub 694 T=0.991 C=0.009
Qatari Global Study-wide 216 T=0.991 C=0.009
SGDP_PRJ Global Study-wide 6 T=0.5 C=0.5
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 4 NC_000004.12:g.17804008T>C
GRCh37.p13 chr 4 NC_000004.11:g.17805631T>C
Gene: DCAF16, DDB1 and CUL4 associated factor 16 (minus strand)
Molecule type Change Amino acid[Codon] SO Term
DCAF16 transcript variant 2 NM_017741.4:c.134A>G N [AAC] > S [AGC] Coding Sequence Variant
DDB1- and CUL4-associated factor 16 NP_060211.3:p.Asn45Ser N (Asn) > S (Ser) Missense Variant
DCAF16 transcript variant 4 NM_001345882.2:c.134A>G N [AAC] > S [AGC] Coding Sequence Variant
DDB1- and CUL4-associated factor 16 NP_001332811.1:p.Asn45Ser N (Asn) > S (Ser) Missense Variant
DCAF16 transcript variant 6 NM_001345885.2:c.134A>G N [AAC] > S [AGC] Coding Sequence Variant
DDB1- and CUL4-associated factor 16 NP_001332814.1:p.Asn45Ser N (Asn) > S (Ser) Missense Variant
DCAF16 transcript variant 5 NM_001345884.2:c.134A>G N [AAC] > S [AGC] Coding Sequence Variant
DDB1- and CUL4-associated factor 16 NP_001332813.1:p.Asn45Ser N (Asn) > S (Ser) Missense Variant
DCAF16 transcript variant 3 NM_001345881.2:c.134A>G N [AAC] > S [AGC] Coding Sequence Variant
DDB1- and CUL4-associated factor 16 NP_001332810.1:p.Asn45Ser N (Asn) > S (Ser) Missense Variant
DCAF16 transcript variant 1 NM_001345880.2:c.134A>G N [AAC] > S [AGC] Coding Sequence Variant
DDB1- and CUL4-associated factor 16 NP_001332809.1:p.Asn45Ser N (Asn) > S (Ser) Missense Variant
DCAF16 transcript variant 9 NR_144301.2:n. N/A Intron Variant
DCAF16 transcript variant 11 NR_144303.2:n. N/A Intron Variant
DCAF16 transcript variant 13 NR_144305.2:n. N/A Intron Variant
DCAF16 transcript variant 18 NR_144310.2:n. N/A Intron Variant
DCAF16 transcript variant X1 XM_047415859.1:c.134A>G N [AAC] > S [AGC] Coding Sequence Variant
DDB1- and CUL4-associated factor 16 isoform X1 XP_047271815.1:p.Asn45Ser N (Asn) > S (Ser) Missense Variant
DCAF16 transcript variant X2 XM_047415860.1:c.134A>G N [AAC] > S [AGC] Coding Sequence Variant
DDB1- and CUL4-associated factor 16 isoform X1 XP_047271816.1:p.Asn45Ser N (Asn) > S (Ser) Missense Variant
DCAF16 transcript variant X3 XM_047415861.1:c.134A>G N [AAC] > S [AGC] Coding Sequence Variant
DDB1- and CUL4-associated factor 16 isoform X1 XP_047271817.1:p.Asn45Ser N (Asn) > S (Ser) Missense 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 T= C
GRCh38.p14 chr 4 NC_000004.12:g.17804008= NC_000004.12:g.17804008T>C
GRCh37.p13 chr 4 NC_000004.11:g.17805631= NC_000004.11:g.17805631T>C
DCAF16 transcript variant 2 NM_017741.4:c.134= NM_017741.4:c.134A>G
DCAF16 transcript variant 2 NM_017741.3:c.134= NM_017741.3:c.134A>G
DCAF16 transcript variant 1 NM_001345880.2:c.134= NM_001345880.2:c.134A>G
DCAF16 transcript variant 1 NM_001345880.1:c.134= NM_001345880.1:c.134A>G
DCAF16 transcript variant 5 NM_001345884.2:c.134= NM_001345884.2:c.134A>G
DCAF16 transcript variant 5 NM_001345884.1:c.134= NM_001345884.1:c.134A>G
DCAF16 transcript variant 4 NM_001345882.2:c.134= NM_001345882.2:c.134A>G
DCAF16 transcript variant 4 NM_001345882.1:c.134= NM_001345882.1:c.134A>G
DCAF16 transcript variant 6 NM_001345885.2:c.134= NM_001345885.2:c.134A>G
DCAF16 transcript variant 6 NM_001345885.1:c.134= NM_001345885.1:c.134A>G
DCAF16 transcript variant 3 NM_001345881.2:c.134= NM_001345881.2:c.134A>G
DCAF16 transcript variant 3 NM_001345881.1:c.134= NM_001345881.1:c.134A>G
DCAF16 transcript variant X1 XM_047415859.1:c.134= XM_047415859.1:c.134A>G
DCAF16 transcript variant X2 XM_047415860.1:c.134= XM_047415860.1:c.134A>G
DCAF16 transcript variant X3 XM_047415861.1:c.134= XM_047415861.1:c.134A>G
DCAF16 transcript variant 12 NR_144304.1:n.1351= NR_144304.1:n.1351A>G
DDB1- and CUL4-associated factor 16 NP_060211.3:p.Asn45= NP_060211.3:p.Asn45Ser
DDB1- and CUL4-associated factor 16 NP_001332809.1:p.Asn45= NP_001332809.1:p.Asn45Ser
DDB1- and CUL4-associated factor 16 NP_001332813.1:p.Asn45= NP_001332813.1:p.Asn45Ser
DDB1- and CUL4-associated factor 16 NP_001332811.1:p.Asn45= NP_001332811.1:p.Asn45Ser
DDB1- and CUL4-associated factor 16 NP_001332814.1:p.Asn45= NP_001332814.1:p.Asn45Ser
DDB1- and CUL4-associated factor 16 NP_001332810.1:p.Asn45= NP_001332810.1:p.Asn45Ser
DDB1- and CUL4-associated factor 16 isoform X1 XP_047271815.1:p.Asn45= XP_047271815.1:p.Asn45Ser
DDB1- and CUL4-associated factor 16 isoform X1 XP_047271816.1:p.Asn45= XP_047271816.1:p.Asn45Ser
DDB1- and CUL4-associated factor 16 isoform X1 XP_047271817.1:p.Asn45= XP_047271817.1:p.Asn45Ser
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#.

64 SubSNP, 11 Frequency submissions
No Submitter Submission ID Date (Build)
1 APPLERA_GI ss48415227 Mar 13, 2006 (126)
2 PERLEGEN ss68892417 May 17, 2007 (127)
3 ILLUMINA ss161082449 Dec 01, 2009 (131)
4 1000GENOMES ss220773183 Jul 14, 2010 (132)
5 NHLBI-ESP ss342160823 May 09, 2011 (134)
6 ILLUMINA ss479281236 Sep 08, 2015 (146)
7 ILLUMINA ss482279224 May 04, 2012 (137)
8 ILLUMINA ss484753642 May 04, 2012 (137)
9 1000GENOMES ss490885003 May 04, 2012 (137)
10 EXOME_CHIP ss491354257 May 04, 2012 (137)
11 ILLUMINA ss534576535 Sep 08, 2015 (146)
12 TISHKOFF ss557347651 Apr 25, 2013 (138)
13 ILLUMINA ss779352453 Aug 21, 2014 (142)
14 ILLUMINA ss780827558 Aug 21, 2014 (142)
15 ILLUMINA ss781708719 Aug 21, 2014 (142)
16 ILLUMINA ss783510373 Aug 21, 2014 (142)
17 ILLUMINA ss834820501 Aug 21, 2014 (142)
18 JMKIDD_LAB ss1067460208 Aug 21, 2014 (142)
19 JMKIDD_LAB ss1071318541 Aug 21, 2014 (142)
20 1000GENOMES ss1308654802 Aug 21, 2014 (142)
21 EVA_EXAC ss1687445655 Apr 01, 2015 (144)
22 ILLUMINA ss1752510565 Sep 08, 2015 (146)
23 ILLUMINA ss1917779148 Feb 12, 2016 (147)
24 WEILL_CORNELL_DGM ss1923062850 Feb 12, 2016 (147)
25 ILLUMINA ss1946111360 Feb 12, 2016 (147)
26 ILLUMINA ss1958665068 Feb 12, 2016 (147)
27 HUMAN_LONGEVITY ss2260855288 Dec 20, 2016 (150)
28 ILLUMINA ss2634089009 Nov 08, 2017 (151)
29 ILLUMINA ss2634089010 Nov 08, 2017 (151)
30 GNOMAD ss2734434167 Nov 08, 2017 (151)
31 GNOMAD ss2747215904 Nov 08, 2017 (151)
32 GNOMAD ss2806256251 Nov 08, 2017 (151)
33 AFFY ss2985287329 Nov 08, 2017 (151)
34 ILLUMINA ss3022352440 Nov 08, 2017 (151)
35 ILLUMINA ss3628913763 Oct 12, 2018 (152)
36 ILLUMINA ss3628913764 Oct 12, 2018 (152)
37 ILLUMINA ss3632027336 Oct 12, 2018 (152)
38 ILLUMINA ss3634943312 Oct 12, 2018 (152)
39 ILLUMINA ss3636644828 Oct 12, 2018 (152)
40 ILLUMINA ss3640650608 Oct 12, 2018 (152)
41 ILLUMINA ss3644844078 Oct 12, 2018 (152)
42 ILLUMINA ss3652835618 Oct 12, 2018 (152)
43 ILLUMINA ss3654057863 Oct 12, 2018 (152)
44 EVA_DECODE ss3711517171 Jul 13, 2019 (153)
45 ILLUMINA ss3726114284 Jul 13, 2019 (153)
46 ILLUMINA ss3744523360 Jul 13, 2019 (153)
47 ILLUMINA ss3745243604 Jul 13, 2019 (153)
48 PAGE_CC ss3771109350 Jul 13, 2019 (153)
49 ILLUMINA ss3772738287 Jul 13, 2019 (153)
50 KHV_HUMAN_GENOMES ss3804600973 Jul 13, 2019 (153)
51 EVA ss3824005964 Apr 26, 2020 (154)
52 EVA ss3825654728 Apr 26, 2020 (154)
53 SGDP_PRJ ss3858340838 Apr 26, 2020 (154)
54 FSA-LAB ss3984279822 Apr 26, 2021 (155)
55 EVA ss3986275737 Apr 26, 2021 (155)
56 TOPMED ss4604718695 Apr 26, 2021 (155)
57 1000G_HIGH_COVERAGE ss5258240920 Oct 13, 2022 (156)
58 EVA ss5347261823 Oct 13, 2022 (156)
59 HUGCELL_USP ss5457119325 Oct 13, 2022 (156)
60 1000G_HIGH_COVERAGE ss5538775878 Oct 13, 2022 (156)
61 SANFORD_IMAGENETICS ss5634462944 Oct 13, 2022 (156)
62 EVA ss5848003370 Oct 13, 2022 (156)
63 EVA ss5862368964 Oct 13, 2022 (156)
64 EVA ss5962842478 Oct 13, 2022 (156)
65 1000Genomes NC_000004.11 - 17805631 Oct 12, 2018 (152)
66 1000Genomes_30x NC_000004.12 - 17804008 Oct 13, 2022 (156)
67 ExAC NC_000004.11 - 17805631 Oct 12, 2018 (152)
68 gnomAD - Genomes NC_000004.12 - 17804008 Apr 26, 2021 (155)
69 gnomAD - Exomes NC_000004.11 - 17805631 Jul 13, 2019 (153)
70 GO Exome Sequencing Project NC_000004.11 - 17805631 Oct 12, 2018 (152)
71 The PAGE Study NC_000004.12 - 17804008 Jul 13, 2019 (153)
72 Qatari NC_000004.11 - 17805631 Apr 26, 2020 (154)
73 SGDP_PRJ NC_000004.11 - 17805631 Apr 26, 2020 (154)
74 TopMed NC_000004.12 - 17804008 Apr 26, 2021 (155)
75 ALFA NC_000004.12 - 17804008 Apr 26, 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
ss161082449, ss484753642 NC_000004.10:17414728:T:C NC_000004.12:17804007:T:C (self)
20010079, 7405531, 3535140, 464196, 5104780, 10357818, ss220773183, ss342160823, ss479281236, ss482279224, ss490885003, ss491354257, ss534576535, ss557347651, ss779352453, ss780827558, ss781708719, ss783510373, ss834820501, ss1067460208, ss1071318541, ss1308654802, ss1687445655, ss1752510565, ss1917779148, ss1923062850, ss1946111360, ss1958665068, ss2634089009, ss2634089010, ss2734434167, ss2747215904, ss2806256251, ss2985287329, ss3022352440, ss3628913763, ss3628913764, ss3632027336, ss3634943312, ss3636644828, ss3640650608, ss3644844078, ss3652835618, ss3654057863, ss3744523360, ss3745243604, ss3772738287, ss3824005964, ss3825654728, ss3858340838, ss3984279822, ss3986275737, ss5347261823, ss5634462944, ss5848003370, ss5962842478 NC_000004.11:17805630:T:C NC_000004.12:17804007:T:C (self)
26301813, 141820608, 330819, 442096251, 3724895631, ss2260855288, ss3711517171, ss3726114284, ss3771109350, ss3804600973, ss4604718695, ss5258240920, ss5457119325, ss5538775878, ss5862368964 NC_000004.12:17804007:T:C NC_000004.12:17804007:T:C (self)
ss48415227, ss68892417 NT_006316.16:8987427:T:C NC_000004.12:17804007:T: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 rs34085539

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