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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.

rs16901958

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr5:44776454 (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
A>G
Variation Type
SNV Single Nucleotide Variation
Frequency
G=0.062065 (16428/264690, TOPMED)
G=0.031418 (6449/205264, ALFA)
G=0.027868 (5715/205076, GENOGRAPHIC) (+ 21 more)
G=0.061127 (8567/140150, GnomAD)
G=0.00290 (82/28258, 14KJPN)
G=0.00316 (53/16760, 8.3KJPN)
G=0.0579 (371/6404, 1000G_30x)
G=0.0551 (276/5008, 1000G)
G=0.0181 (81/4480, Estonian)
G=0.0275 (106/3854, ALSPAC)
G=0.0280 (104/3708, TWINSUK)
G=0.0007 (2/2922, KOREAN)
G=0.0389 (81/2084, HGDP_Stanford)
G=0.0011 (2/1832, Korea1K)
G=0.0789 (109/1382, HapMap)
G=0.025 (25/998, GoNL)
G=0.014 (9/626, Chileans)
G=0.018 (11/600, NorthernSweden)
G=0.032 (7/216, Qatari)
G=0.014 (3/216, Vietnamese)
G=0.03 (2/76, Ancient Sardinia)
A=0.42 (22/52, SGDP_PRJ)
A=0.5 (4/8, Siberian)
G=0.5 (4/8, Siberian)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
MRPS30-DT : 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 205264 A=0.968582 G=0.031418
European Sub 174150 A=0.974436 G=0.025564
African Sub 10220 A=0.85665 G=0.14335
African Others Sub 360 A=0.842 G=0.158
African American Sub 9860 A=0.8572 G=0.1428
Asian Sub 750 A=0.969 G=0.031
East Asian Sub 572 A=0.979 G=0.021
Other Asian Sub 178 A=0.938 G=0.062
Latin American 1 Sub 910 A=0.947 G=0.053
Latin American 2 Sub 7050 A=0.9820 G=0.0180
South Asian Sub 5054 A=0.9899 G=0.0101
Other Sub 7130 A=0.9603 G=0.0397


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 A=0.937935 G=0.062065
Allele Frequency Aggregator Total Global 205264 A=0.968582 G=0.031418
Allele Frequency Aggregator European Sub 174150 A=0.974436 G=0.025564
Allele Frequency Aggregator African Sub 10220 A=0.85665 G=0.14335
Allele Frequency Aggregator Other Sub 7130 A=0.9603 G=0.0397
Allele Frequency Aggregator Latin American 2 Sub 7050 A=0.9820 G=0.0180
Allele Frequency Aggregator South Asian Sub 5054 A=0.9899 G=0.0101
Allele Frequency Aggregator Latin American 1 Sub 910 A=0.947 G=0.053
Allele Frequency Aggregator Asian Sub 750 A=0.969 G=0.031
Genographic Project Global Study-wide 205076 A=0.972132 G=0.027868
gnomAD - Genomes Global Study-wide 140150 A=0.938873 G=0.061127
gnomAD - Genomes European Sub 75926 A=0.97532 G=0.02468
gnomAD - Genomes African Sub 41984 A=0.85606 G=0.14394
gnomAD - Genomes American Sub 13640 A=0.96935 G=0.03065
gnomAD - Genomes Ashkenazi Jewish Sub 3318 A=0.9720 G=0.0280
gnomAD - Genomes East Asian Sub 3130 A=0.9936 G=0.0064
gnomAD - Genomes Other Sub 2152 A=0.9447 G=0.0553
14KJPN JAPANESE Study-wide 28258 A=0.99710 G=0.00290
8.3KJPN JAPANESE Study-wide 16760 A=0.99684 G=0.00316
1000Genomes_30x Global Study-wide 6404 A=0.9421 G=0.0579
1000Genomes_30x African Sub 1786 A=0.8354 G=0.1646
1000Genomes_30x Europe Sub 1266 A=0.9739 G=0.0261
1000Genomes_30x South Asian Sub 1202 A=0.9942 G=0.0058
1000Genomes_30x East Asian Sub 1170 A=0.9957 G=0.0043
1000Genomes_30x American Sub 980 A=0.967 G=0.033
1000Genomes Global Study-wide 5008 A=0.9449 G=0.0551
1000Genomes African Sub 1322 A=0.8336 G=0.1664
1000Genomes East Asian Sub 1008 A=0.9960 G=0.0040
1000Genomes Europe Sub 1006 A=0.9742 G=0.0258
1000Genomes South Asian Sub 978 A=0.995 G=0.005
1000Genomes American Sub 694 A=0.970 G=0.030
Genetic variation in the Estonian population Estonian Study-wide 4480 A=0.9819 G=0.0181
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 A=0.9725 G=0.0275
UK 10K study - Twins TWIN COHORT Study-wide 3708 A=0.9720 G=0.0280
KOREAN population from KRGDB KOREAN Study-wide 2922 A=0.9993 G=0.0007
HGDP-CEPH-db Supplement 1 Global Study-wide 2084 A=0.9611 G=0.0389
HGDP-CEPH-db Supplement 1 Est_Asia Sub 470 A=0.996 G=0.004
HGDP-CEPH-db Supplement 1 Central_South_Asia Sub 414 A=0.986 G=0.014
HGDP-CEPH-db Supplement 1 Middle_Est Sub 350 A=0.991 G=0.009
HGDP-CEPH-db Supplement 1 Europe Sub 320 A=0.984 G=0.016
HGDP-CEPH-db Supplement 1 Africa Sub 242 A=0.736 G=0.264
HGDP-CEPH-db Supplement 1 America Sub 216 A=1.000 G=0.000
HGDP-CEPH-db Supplement 1 Oceania Sub 72 A=0.99 G=0.01
Korean Genome Project KOREAN Study-wide 1832 A=0.9989 G=0.0011
HapMap Global Study-wide 1382 A=0.9211 G=0.0789
HapMap African Sub 692 A=0.873 G=0.127
HapMap American Sub 424 A=0.960 G=0.040
HapMap Europe Sub 176 A=0.977 G=0.023
HapMap Asian Sub 90 A=1.00 G=0.00
Genome of the Netherlands Release 5 Genome of the Netherlands Study-wide 998 A=0.975 G=0.025
Chileans Chilean Study-wide 626 A=0.986 G=0.014
Northern Sweden ACPOP Study-wide 600 A=0.982 G=0.018
Qatari Global Study-wide 216 A=0.968 G=0.032
A Vietnamese Genetic Variation Database Global Study-wide 216 A=0.986 G=0.014
Ancient Sardinia genome-wide 1240k capture data generation and analysis Global Study-wide 76 A=0.97 G=0.03
SGDP_PRJ Global Study-wide 52 A=0.42 G=0.58
Siberian Global Study-wide 8 A=0.5 G=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 5 NC_000005.10:g.44776454A>G
GRCh37.p13 chr 5 NC_000005.9:g.44776556A>G
Gene: MRPS30-DT, MRPS30 divergent transcript (minus strand)
Molecule type Change Amino acid[Codon] SO Term
MRPS30-DT transcript variant 1 NR_109862.1:n. N/A Intron Variant
MRPS30-DT transcript variant 2 NR_109863.1:n. N/A Intron Variant
MRPS30-DT transcript variant 3 NR_109864.1:n. N/A Intron Variant
MRPS30-DT transcript variant 4 NR_109865.1:n. N/A Intron 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 A= G
GRCh38.p14 chr 5 NC_000005.10:g.44776454= NC_000005.10:g.44776454A>G
GRCh37.p13 chr 5 NC_000005.9:g.44776556= NC_000005.9:g.44776556A>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#.

96 SubSNP, 23 Frequency submissions
No Submitter Submission ID Date (Build)
1 PERLEGEN ss23412736 Sep 20, 2004 (123)
2 ABI ss42451362 Mar 14, 2006 (126)
3 AFFY ss66308284 Dec 01, 2006 (127)
4 ILLUMINA ss67155229 Dec 01, 2006 (127)
5 ILLUMINA ss67501537 Dec 01, 2006 (127)
6 ILLUMINA ss68164727 Dec 12, 2006 (127)
7 ILLUMINA ss70643642 May 26, 2008 (130)
8 ILLUMINA ss71196900 May 17, 2007 (127)
9 ILLUMINA ss75920868 Dec 06, 2007 (129)
10 AFFY ss75985759 Dec 06, 2007 (129)
11 KRIBB_YJKIM ss85333940 Dec 16, 2007 (130)
12 HUMANGENOME_JCVI ss98718487 Feb 06, 2009 (130)
13 ILLUMINA-UK ss116594876 Feb 14, 2009 (130)
14 ILLUMINA ss153572660 Dec 01, 2009 (131)
15 ILLUMINA ss159296589 Dec 01, 2009 (131)
16 ILLUMINA ss160394517 Dec 01, 2009 (131)
17 AFFY ss170037329 Jul 04, 2010 (132)
18 ILLUMINA ss172653128 Jul 04, 2010 (132)
19 BUSHMAN ss200189701 Jul 04, 2010 (132)
20 1000GENOMES ss221655888 Jul 14, 2010 (132)
21 1000GENOMES ss232927946 Jul 14, 2010 (132)
22 PJP ss293579572 May 09, 2011 (134)
23 ILLUMINA ss480097340 May 04, 2012 (137)
24 ILLUMINA ss480106205 May 04, 2012 (137)
25 ILLUMINA ss480795042 Sep 08, 2015 (146)
26 ILLUMINA ss484846529 May 04, 2012 (137)
27 ILLUMINA ss536916988 Sep 08, 2015 (146)
28 TISHKOFF ss558364583 Apr 25, 2013 (138)
29 SSMP ss652222489 Apr 25, 2013 (138)
30 ILLUMINA ss779034721 Aug 21, 2014 (142)
31 ILLUMINA ss782869803 Aug 21, 2014 (142)
32 ILLUMINA ss783833902 Aug 21, 2014 (142)
33 ILLUMINA ss832123957 Apr 01, 2015 (144)
34 ILLUMINA ss832808684 Aug 21, 2014 (142)
35 ILLUMINA ss833399514 Aug 21, 2014 (142)
36 ILLUMINA ss834497487 Aug 21, 2014 (142)
37 EVA-GONL ss981512690 Aug 21, 2014 (142)
38 JMKIDD_LAB ss1072592598 Aug 21, 2014 (142)
39 1000GENOMES ss1314893570 Aug 21, 2014 (142)
40 EVA_DECODE ss1591036199 Apr 01, 2015 (144)
41 EVA_UK10K_ALSPAC ss1612786528 Apr 01, 2015 (144)
42 EVA_UK10K_TWINSUK ss1655780561 Apr 01, 2015 (144)
43 EVA_SVP ss1712761122 Apr 01, 2015 (144)
44 ILLUMINA ss1752576334 Sep 08, 2015 (146)
45 HAMMER_LAB ss1803447055 Sep 08, 2015 (146)
46 WEILL_CORNELL_DGM ss1924772893 Feb 12, 2016 (147)
47 JJLAB ss2022990359 Sep 14, 2016 (149)
48 USC_VALOUEV ss2151142222 Dec 20, 2016 (150)
49 HUMAN_LONGEVITY ss2273386528 Dec 20, 2016 (150)
50 ILLUMINA ss2634274437 Nov 08, 2017 (151)
51 GNOMAD ss2823974431 Nov 08, 2017 (151)
52 SWEGEN ss2996840137 Nov 08, 2017 (151)
53 ILLUMINA ss3629226910 Oct 12, 2018 (152)
54 ILLUMINA ss3632201816 Oct 12, 2018 (152)
55 ILLUMINA ss3633372912 Oct 12, 2018 (152)
56 ILLUMINA ss3634093450 Oct 12, 2018 (152)
57 ILLUMINA ss3635000320 Oct 12, 2018 (152)
58 ILLUMINA ss3635775509 Oct 12, 2018 (152)
59 ILLUMINA ss3636710991 Oct 12, 2018 (152)
60 ILLUMINA ss3637528110 Oct 12, 2018 (152)
61 ILLUMINA ss3638551168 Oct 12, 2018 (152)
62 ILLUMINA ss3639278228 Oct 12, 2018 (152)
63 ILLUMINA ss3639936806 Oct 12, 2018 (152)
64 ILLUMINA ss3640707613 Oct 12, 2018 (152)
65 ILLUMINA ss3643497336 Oct 12, 2018 (152)
66 ILLUMINA ss3643982393 Oct 12, 2018 (152)
67 BIOINF_KMB_FNS_UNIBA ss3645875238 Oct 12, 2018 (152)
68 URBANLAB ss3648045777 Oct 12, 2018 (152)
69 EGCUT_WGS ss3664738933 Jul 13, 2019 (153)
70 EVA_DECODE ss3714588246 Jul 13, 2019 (153)
71 ACPOP ss3732312918 Jul 13, 2019 (153)
72 ILLUMINA ss3745300523 Jul 13, 2019 (153)
73 EVA ss3763370491 Jul 13, 2019 (153)
74 ILLUMINA ss3772794751 Jul 13, 2019 (153)
75 KHV_HUMAN_GENOMES ss3806544877 Jul 13, 2019 (153)
76 HGDP ss3847789178 Apr 26, 2020 (154)
77 SGDP_PRJ ss3861745868 Apr 26, 2020 (154)
78 KRGDB ss3908233747 Apr 26, 2020 (154)
79 KOGIC ss3956544710 Apr 26, 2020 (154)
80 EVA ss3985138556 Apr 26, 2021 (155)
81 EVA ss4017204634 Apr 26, 2021 (155)
82 TOPMED ss4658138441 Apr 26, 2021 (155)
83 TOMMO_GENOMICS ss5171497326 Apr 26, 2021 (155)
84 1000G_HIGH_COVERAGE ss5263758547 Oct 13, 2022 (156)
85 GENOGRAPHIC ss5314505797 Oct 13, 2022 (156)
86 EVA ss5315048952 Oct 13, 2022 (156)
87 EVA ss5357234164 Oct 13, 2022 (156)
88 HUGCELL_USP ss5462001722 Oct 13, 2022 (156)
89 EVA ss5508004425 Oct 13, 2022 (156)
90 1000G_HIGH_COVERAGE ss5547280156 Oct 13, 2022 (156)
91 SANFORD_IMAGENETICS ss5637700962 Oct 13, 2022 (156)
92 TOMMO_GENOMICS ss5707479277 Oct 13, 2022 (156)
93 EVA ss5799647505 Oct 13, 2022 (156)
94 EVA ss5834862544 Oct 13, 2022 (156)
95 EVA ss5893982688 Oct 13, 2022 (156)
96 EVA ss5966123626 Oct 13, 2022 (156)
97 1000Genomes NC_000005.9 - 44776556 Oct 12, 2018 (152)
98 1000Genomes_30x NC_000005.10 - 44776454 Oct 13, 2022 (156)
99 The Avon Longitudinal Study of Parents and Children NC_000005.9 - 44776556 Oct 12, 2018 (152)
100 Chileans NC_000005.9 - 44776556 Apr 26, 2020 (154)
101 Genetic variation in the Estonian population NC_000005.9 - 44776556 Oct 12, 2018 (152)
102 Genographic Project NC_000005.10 - 44776454 Oct 13, 2022 (156)
103 gnomAD - Genomes NC_000005.10 - 44776454 Apr 26, 2021 (155)
104 Genome of the Netherlands Release 5 NC_000005.9 - 44776556 Apr 26, 2020 (154)
105 HGDP-CEPH-db Supplement 1 NC_000005.8 - 44812313 Apr 26, 2020 (154)
106 HapMap NC_000005.10 - 44776454 Apr 26, 2020 (154)
107 KOREAN population from KRGDB NC_000005.9 - 44776556 Apr 26, 2020 (154)
108 Korean Genome Project NC_000005.10 - 44776454 Apr 26, 2020 (154)
109 Northern Sweden NC_000005.9 - 44776556 Jul 13, 2019 (153)
110 Ancient Sardinia genome-wide 1240k capture data generation and analysis NC_000005.9 - 44776556 Apr 26, 2021 (155)
111 Qatari NC_000005.9 - 44776556 Apr 26, 2020 (154)
112 SGDP_PRJ NC_000005.9 - 44776556 Apr 26, 2020 (154)
113 Siberian NC_000005.9 - 44776556 Apr 26, 2020 (154)
114 8.3KJPN NC_000005.9 - 44776556 Apr 26, 2021 (155)
115 14KJPN NC_000005.10 - 44776454 Oct 13, 2022 (156)
116 TopMed NC_000005.10 - 44776454 Apr 26, 2021 (155)
117 UK 10K study - Twins NC_000005.9 - 44776556 Oct 12, 2018 (152)
118 A Vietnamese Genetic Variation Database NC_000005.9 - 44776556 Jul 13, 2019 (153)
119 ALFA NC_000005.10 - 44776454 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).

Associated ID History Updated (Build)
rs61175282 May 26, 2008 (130)
Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
467070, ss66308284, ss75985759, ss116594876, ss160394517, ss170037329, ss200189701, ss293579572, ss480097340, ss1591036199, ss1712761122, ss3639278228, ss3639936806, ss3643497336, ss3643982393, ss3847789178 NC_000005.8:44812312:A:G NC_000005.10:44776453:A:G (self)
26486584, 14729254, 345019, 10477181, 6547028, 15411141, 5597783, 364483, 6814823, 13762848, 3658576, 29466633, 14729254, 3273690, ss221655888, ss232927946, ss480106205, ss480795042, ss484846529, ss536916988, ss558364583, ss652222489, ss779034721, ss782869803, ss783833902, ss832123957, ss832808684, ss833399514, ss834497487, ss981512690, ss1072592598, ss1314893570, ss1612786528, ss1655780561, ss1752576334, ss1803447055, ss1924772893, ss2022990359, ss2151142222, ss2634274437, ss2823974431, ss2996840137, ss3629226910, ss3632201816, ss3633372912, ss3634093450, ss3635000320, ss3635775509, ss3636710991, ss3637528110, ss3638551168, ss3640707613, ss3664738933, ss3732312918, ss3745300523, ss3763370491, ss3772794751, ss3861745868, ss3908233747, ss3985138556, ss4017204634, ss5171497326, ss5315048952, ss5357234164, ss5508004425, ss5637700962, ss5799647505, ss5834862544, ss5966123626 NC_000005.9:44776555:A:G NC_000005.10:44776453:A:G (self)
34806091, 86302, 187105788, 2858434, 12922711, 41316381, 495515998, 11644107642, ss2273386528, ss3645875238, ss3648045777, ss3714588246, ss3806544877, ss3956544710, ss4658138441, ss5263758547, ss5314505797, ss5462001722, ss5547280156, ss5707479277, ss5893982688 NC_000005.10:44776453:A:G NC_000005.10:44776453:A:G (self)
ss23412736, ss42451362, ss67155229, ss67501537, ss68164727, ss70643642, ss71196900, ss75920868, ss85333940, ss98718487, ss153572660, ss159296589, ss172653128 NT_006576.16:44766555:A:G NC_000005.10:44776453:A:G (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 rs16901958

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