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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.

rs17676109

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr12:62656471 (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>G
Variation Type
SNV Single Nucleotide Variation
Frequency
G=0.034531 (9140/264690, TOPMED)
G=0.037974 (5326/140254, GnomAD)
G=0.04764 (1209/25378, ALFA) (+ 16 more)
G=0.0184 (118/6404, 1000G_30x)
G=0.0184 (92/5008, 1000G)
G=0.0408 (183/4480, Estonian)
G=0.0555 (214/3854, ALSPAC)
G=0.0480 (178/3708, TWINSUK)
G=0.0003 (1/2922, KOREAN)
G=0.0431 (49/1136, Daghestan)
G=0.054 (54/998, GoNL)
G=0.070 (42/600, NorthernSweden)
G=0.033 (11/330, HapMap)
G=0.019 (4/216, Qatari)
G=0.10 (4/40, GENOME_DK)
T=0.50 (10/20, SGDP_PRJ)
G=0.50 (10/20, SGDP_PRJ)
T=0.5 (4/8, Siberian)
G=0.5 (4/8, Siberian)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
PPM1H : 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 25472 T=0.95218 G=0.04782
European Sub 20578 T=0.94582 G=0.05418
African Sub 2950 T=0.9864 G=0.0136
African Others Sub 114 T=1.000 G=0.000
African American Sub 2836 T=0.9859 G=0.0141
Asian Sub 114 T=1.000 G=0.000
East Asian Sub 88 T=1.00 G=0.00
Other Asian Sub 26 T=1.00 G=0.00
Latin American 1 Sub 146 T=0.979 G=0.021
Latin American 2 Sub 610 T=0.980 G=0.020
South Asian Sub 100 T=0.96 G=0.04
Other Sub 974 T=0.955 G=0.045


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=0.965469 G=0.034531
gnomAD - Genomes Global Study-wide 140254 T=0.962026 G=0.037974
gnomAD - Genomes European Sub 75932 T=0.94558 G=0.05442
gnomAD - Genomes African Sub 42060 T=0.99042 G=0.00958
gnomAD - Genomes American Sub 13656 T=0.97327 G=0.02673
gnomAD - Genomes Ashkenazi Jewish Sub 3320 T=0.8985 G=0.1015
gnomAD - Genomes East Asian Sub 3132 T=0.9984 G=0.0016
gnomAD - Genomes Other Sub 2154 T=0.9610 G=0.0390
Allele Frequency Aggregator Total Global 25378 T=0.95236 G=0.04764
Allele Frequency Aggregator European Sub 20502 T=0.94591 G=0.05409
Allele Frequency Aggregator African Sub 2950 T=0.9864 G=0.0136
Allele Frequency Aggregator Other Sub 956 T=0.957 G=0.043
Allele Frequency Aggregator Latin American 2 Sub 610 T=0.980 G=0.020
Allele Frequency Aggregator Latin American 1 Sub 146 T=0.979 G=0.021
Allele Frequency Aggregator Asian Sub 114 T=1.000 G=0.000
Allele Frequency Aggregator South Asian Sub 100 T=0.96 G=0.04
1000Genomes_30x Global Study-wide 6404 T=0.9816 G=0.0184
1000Genomes_30x African Sub 1786 T=0.9972 G=0.0028
1000Genomes_30x Europe Sub 1266 T=0.9487 G=0.0513
1000Genomes_30x South Asian Sub 1202 T=0.9759 G=0.0241
1000Genomes_30x East Asian Sub 1170 T=0.9991 G=0.0009
1000Genomes_30x American Sub 980 T=0.982 G=0.018
1000Genomes Global Study-wide 5008 T=0.9816 G=0.0184
1000Genomes African Sub 1322 T=0.9970 G=0.0030
1000Genomes East Asian Sub 1008 T=0.9990 G=0.0010
1000Genomes Europe Sub 1006 T=0.9503 G=0.0497
1000Genomes South Asian Sub 978 T=0.975 G=0.025
1000Genomes American Sub 694 T=0.981 G=0.019
Genetic variation in the Estonian population Estonian Study-wide 4480 T=0.9592 G=0.0408
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 T=0.9445 G=0.0555
UK 10K study - Twins TWIN COHORT Study-wide 3708 T=0.9520 G=0.0480
KOREAN population from KRGDB KOREAN Study-wide 2922 T=0.9997 G=0.0003
Genome-wide autozygosity in Daghestan Global Study-wide 1136 T=0.9569 G=0.0431
Genome-wide autozygosity in Daghestan Daghestan Sub 628 T=0.955 G=0.045
Genome-wide autozygosity in Daghestan Near_East Sub 144 T=0.917 G=0.083
Genome-wide autozygosity in Daghestan Central Asia Sub 122 T=0.984 G=0.016
Genome-wide autozygosity in Daghestan Europe Sub 108 T=0.972 G=0.028
Genome-wide autozygosity in Daghestan South Asian Sub 98 T=0.98 G=0.02
Genome-wide autozygosity in Daghestan Caucasus Sub 36 T=0.94 G=0.06
Genome of the Netherlands Release 5 Genome of the Netherlands Study-wide 998 T=0.946 G=0.054
Northern Sweden ACPOP Study-wide 600 T=0.930 G=0.070
HapMap Global Study-wide 330 T=0.967 G=0.033
HapMap African Sub 120 T=1.000 G=0.000
HapMap American Sub 120 T=0.908 G=0.092
HapMap Asian Sub 90 T=1.00 G=0.00
Qatari Global Study-wide 216 T=0.981 G=0.019
The Danish reference pan genome Danish Study-wide 40 T=0.90 G=0.10
SGDP_PRJ Global Study-wide 20 T=0.50 G=0.50
Siberian Global Study-wide 8 T=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 12 NC_000012.12:g.62656471T>G
GRCh37.p13 chr 12 NC_000012.11:g.63050251T>G
Gene: PPM1H, protein phosphatase, Mg2+/Mn2+ dependent 1H (minus strand)
Molecule type Change Amino acid[Codon] SO Term
PPM1H transcript NM_020700.2:c.1398-7835A>C N/A Intron Variant
PPM1H transcript variant X1 XM_011538578.3:c.1284-783…

XM_011538578.3:c.1284-7835A>C

 		N/A Intron Variant
PPM1H transcript variant X2 XM_017019676.3:c. N/A Genic Downstream 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 T= G
GRCh38.p14 chr 12 NC_000012.12:g.62656471= NC_000012.12:g.62656471T>G
GRCh37.p13 chr 12 NC_000012.11:g.63050251= NC_000012.11:g.63050251T>G
PPM1H transcript NM_020700.1:c.1398-7835= NM_020700.1:c.1398-7835A>C
PPM1H transcript NM_020700.2:c.1398-7835= NM_020700.2:c.1398-7835A>C
PPM1H transcript variant X1 XM_011538578.3:c.1284-7835= XM_011538578.3:c.1284-7835A>C
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#.

45 SubSNP, 17 Frequency submissions
No Submitter Submission ID Date (Build)
1 PERLEGEN ss24388012 Sep 20, 2004 (123)
2 PERLEGEN ss69110833 May 17, 2007 (127)
3 COMPLETE_GENOMICS ss175153803 Jul 04, 2010 (132)
4 1000GENOMES ss235961568 Jul 15, 2010 (132)
5 SSMP ss658772982 Apr 25, 2013 (138)
6 EVA-GONL ss989611711 Aug 21, 2014 (142)
7 JMKIDD_LAB ss1078516071 Aug 21, 2014 (142)
8 1000GENOMES ss1345321447 Aug 21, 2014 (142)
9 HAMMER_LAB ss1397635448 Sep 08, 2015 (146)
10 EVA_GENOME_DK ss1576325881 Apr 01, 2015 (144)
11 EVA_DECODE ss1599287227 Apr 01, 2015 (144)
12 EVA_UK10K_ALSPAC ss1628747386 Apr 01, 2015 (144)
13 EVA_UK10K_TWINSUK ss1671741419 Apr 01, 2015 (144)
14 WEILL_CORNELL_DGM ss1932975552 Feb 12, 2016 (147)
15 JJLAB ss2027237586 Sep 14, 2016 (149)
16 USC_VALOUEV ss2155579590 Dec 20, 2016 (150)
17 HUMAN_LONGEVITY ss2190421108 Dec 20, 2016 (150)
18 GNOMAD ss2911397397 Nov 08, 2017 (151)
19 AFFY ss2984983003 Nov 08, 2017 (151)
20 AFFY ss2985618712 Nov 08, 2017 (151)
21 SWEGEN ss3009815715 Nov 08, 2017 (151)
22 BIOINF_KMB_FNS_UNIBA ss3027428118 Nov 08, 2017 (151)
23 CSHL ss3350098329 Nov 08, 2017 (151)
24 ILLUMINA ss3653752195 Oct 12, 2018 (152)
25 EGCUT_WGS ss3677086307 Jul 13, 2019 (153)
26 EVA_DECODE ss3693820153 Jul 13, 2019 (153)
27 ACPOP ss3739087727 Jul 13, 2019 (153)
28 EVA ss3750571431 Jul 13, 2019 (153)
29 KHV_HUMAN_GENOMES ss3815901934 Jul 13, 2019 (153)
30 SGDP_PRJ ss3878433336 Apr 27, 2020 (154)
31 KRGDB ss3927092247 Apr 27, 2020 (154)
32 TOPMED ss4921027701 Apr 27, 2021 (155)
33 EVA ss5237512730 Apr 27, 2021 (155)
34 1000G_HIGH_COVERAGE ss5291080234 Oct 16, 2022 (156)
35 EVA ss5406125950 Oct 16, 2022 (156)
36 HUGCELL_USP ss5485799742 Oct 16, 2022 (156)
37 1000G_HIGH_COVERAGE ss5588704333 Oct 16, 2022 (156)
38 SANFORD_IMAGENETICS ss5624303431 Oct 16, 2022 (156)
39 SANFORD_IMAGENETICS ss5653304828 Oct 16, 2022 (156)
40 EVA ss5838068242 Oct 16, 2022 (156)
41 EVA ss5847410154 Oct 16, 2022 (156)
42 EVA ss5847673372 Oct 16, 2022 (156)
43 EVA ss5904696251 Oct 16, 2022 (156)
44 EVA ss5944672361 Oct 16, 2022 (156)
45 EVA ss5979393726 Oct 16, 2022 (156)
46 1000Genomes NC_000012.11 - 63050251 Oct 12, 2018 (152)
47 1000Genomes_30x NC_000012.12 - 62656471 Oct 16, 2022 (156)
48 The Avon Longitudinal Study of Parents and Children NC_000012.11 - 63050251 Oct 12, 2018 (152)
49 Genome-wide autozygosity in Daghestan NC_000012.10 - 61336518 Apr 27, 2020 (154)
50 Genetic variation in the Estonian population NC_000012.11 - 63050251 Oct 12, 2018 (152)
51 The Danish reference pan genome NC_000012.11 - 63050251 Apr 27, 2020 (154)
52 gnomAD - Genomes NC_000012.12 - 62656471 Apr 27, 2021 (155)
53 Genome of the Netherlands Release 5 NC_000012.11 - 63050251 Apr 27, 2020 (154)
54 HapMap NC_000012.12 - 62656471 Apr 27, 2020 (154)
55 KOREAN population from KRGDB NC_000012.11 - 63050251 Apr 27, 2020 (154)
56 Northern Sweden NC_000012.11 - 63050251 Jul 13, 2019 (153)
57 Qatari NC_000012.11 - 63050251 Apr 27, 2020 (154)
58 SGDP_PRJ NC_000012.11 - 63050251 Apr 27, 2020 (154)
59 Siberian NC_000012.11 - 63050251 Apr 27, 2020 (154)
60 TopMed NC_000012.12 - 62656471 Apr 27, 2021 (155)
61 UK 10K study - Twins NC_000012.11 - 63050251 Oct 12, 2018 (152)
62 ALFA NC_000012.12 - 62656471 Apr 27, 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
106330, ss175153803, ss1397635448, ss1599287227 NC_000012.10:61336517:T:G NC_000012.12:62656470:T:G (self)
58081554, 32247694, 22824555, 2992729, 14388781, 34269641, 12372592, 15017482, 30450316, 8095944, 32247694, ss235961568, ss658772982, ss989611711, ss1078516071, ss1345321447, ss1576325881, ss1628747386, ss1671741419, ss1932975552, ss2027237586, ss2155579590, ss2911397397, ss2984983003, ss2985618712, ss3009815715, ss3350098329, ss3653752195, ss3677086307, ss3739087727, ss3750571431, ss3878433336, ss3927092247, ss5237512730, ss5406125950, ss5624303431, ss5653304828, ss5838068242, ss5847410154, ss5847673372, ss5944672361, ss5979393726 NC_000012.11:63050250:T:G NC_000012.12:62656470:T:G (self)
76230268, 409615809, 831561, 136573358, 4446129852, ss2190421108, ss3027428118, ss3693820153, ss3815901934, ss4921027701, ss5291080234, ss5485799742, ss5588704333, ss5904696251 NC_000012.12:62656470:T:G NC_000012.12:62656470:T:G (self)
ss24388012, ss69110833 NT_029419.12:25193556:T:G NC_000012.12:62656470:T: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 rs17676109

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