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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.

rs12985970

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr19:847993 (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
C>G / C>T
Variation Type
SNV Single Nucleotide Variation
Frequency
T=0.004200 (816/194292, GnomAD_exome)
T=0.004898 (687/140262, GnomAD)
T=0.00607 (288/47426, ExAC) (+ 12 more)
T=0.00400 (111/27740, ALFA)
T=0.00533 (69/12944, GO-ESP)
T=0.0008 (5/6404, 1000G_30x)
T=0.0008 (4/5008, 1000G)
T=0.0138 (62/4480, Estonian)
T=0.0070 (27/3854, ALSPAC)
T=0.0049 (18/3708, TWINSUK)
T=0.020 (12/600, NorthernSweden)
C=0.5 (1/2, SGDP_PRJ)
T=0.5 (1/2, SGDP_PRJ)
C=0.5 (1/2, Siberian)
T=0.5 (1/2, Siberian)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
PRTN3 : 3 Prime UTR 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 27740 C=0.99600 G=0.00000, T=0.00400
European Sub 20220 C=0.99505 G=0.00000, T=0.00495
African Sub 3536 C=0.9997 G=0.0000, T=0.0003
African Others Sub 122 C=1.000 G=0.000, T=0.000
African American Sub 3414 C=0.9997 G=0.0000, T=0.0003
Asian Sub 168 C=1.000 G=0.000, T=0.000
East Asian Sub 112 C=1.000 G=0.000, T=0.000
Other Asian Sub 56 C=1.00 G=0.00, T=0.00
Latin American 1 Sub 144 C=1.000 G=0.000, T=0.000
Latin American 2 Sub 610 C=1.000 G=0.000, T=0.000
South Asian Sub 98 C=1.00 G=0.00, T=0.00
Other Sub 2964 C=0.9966 G=0.0000, T=0.0034


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
gnomAD - Exomes Global Study-wide 194292 C=0.995800 T=0.004200
gnomAD - Exomes European Sub 98172 C=0.99251 T=0.00749
gnomAD - Exomes Asian Sub 41164 C=0.99976 T=0.00024
gnomAD - Exomes American Sub 29612 C=0.99892 T=0.00108
gnomAD - Exomes African Sub 11464 C=0.99860 T=0.00140
gnomAD - Exomes Ashkenazi Jewish Sub 8854 C=0.9997 T=0.0003
gnomAD - Exomes Other Sub 5026 C=0.9960 T=0.0040
gnomAD - Genomes Global Study-wide 140262 C=0.995102 T=0.004898
gnomAD - Genomes European Sub 75940 C=0.99214 T=0.00786
gnomAD - Genomes African Sub 42046 C=0.99860 T=0.00140
gnomAD - Genomes American Sub 13668 C=0.99846 T=0.00154
gnomAD - Genomes Ashkenazi Jewish Sub 3324 C=0.9985 T=0.0015
gnomAD - Genomes East Asian Sub 3130 C=1.0000 T=0.0000
gnomAD - Genomes Other Sub 2154 C=0.9977 T=0.0023
ExAC Global Study-wide 47426 C=0.99393 T=0.00607
ExAC Europe Sub 25660 C=0.98983 T=0.01017
ExAC Asian Sub 13258 C=0.99940 T=0.00060
ExAC African Sub 4126 C=0.9983 T=0.0017
ExAC American Sub 4034 C=0.9975 T=0.0025
ExAC Other Sub 348 C=0.994 T=0.006
Allele Frequency Aggregator Total Global 27740 C=0.99600 G=0.00000, T=0.00400
Allele Frequency Aggregator European Sub 20220 C=0.99505 G=0.00000, T=0.00495
Allele Frequency Aggregator African Sub 3536 C=0.9997 G=0.0000, T=0.0003
Allele Frequency Aggregator Other Sub 2964 C=0.9966 G=0.0000, T=0.0034
Allele Frequency Aggregator Latin American 2 Sub 610 C=1.000 G=0.000, T=0.000
Allele Frequency Aggregator Asian Sub 168 C=1.000 G=0.000, T=0.000
Allele Frequency Aggregator Latin American 1 Sub 144 C=1.000 G=0.000, T=0.000
Allele Frequency Aggregator South Asian Sub 98 C=1.00 G=0.00, T=0.00
GO Exome Sequencing Project Global Study-wide 12944 C=0.99467 T=0.00533
GO Exome Sequencing Project European American Sub 8572 C=0.9927 T=0.0073
GO Exome Sequencing Project African American Sub 4372 C=0.9986 T=0.0014
1000Genomes_30x Global Study-wide 6404 C=0.9992 T=0.0008
1000Genomes_30x African Sub 1786 C=1.0000 T=0.0000
1000Genomes_30x Europe Sub 1266 C=0.9961 T=0.0039
1000Genomes_30x South Asian Sub 1202 C=1.0000 T=0.0000
1000Genomes_30x East Asian Sub 1170 C=1.0000 T=0.0000
1000Genomes_30x American Sub 980 C=1.000 T=0.000
1000Genomes Global Study-wide 5008 C=0.9992 T=0.0008
1000Genomes African Sub 1322 C=1.0000 T=0.0000
1000Genomes East Asian Sub 1008 C=1.0000 T=0.0000
1000Genomes Europe Sub 1006 C=0.9960 T=0.0040
1000Genomes South Asian Sub 978 C=1.000 T=0.000
1000Genomes American Sub 694 C=1.000 T=0.000
Genetic variation in the Estonian population Estonian Study-wide 4480 C=0.9862 T=0.0138
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 C=0.9930 T=0.0070
UK 10K study - Twins TWIN COHORT Study-wide 3708 C=0.9951 T=0.0049
Northern Sweden ACPOP Study-wide 600 C=0.980 T=0.020
SGDP_PRJ Global Study-wide 2 C=0.5 T=0.5
Siberian Global Study-wide 2 C=0.5 T=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 19 NC_000019.10:g.847993C>G
GRCh38.p14 chr 19 NC_000019.10:g.847993C>T
GRCh37.p13 chr 19 NC_000019.9:g.847993C>G
GRCh37.p13 chr 19 NC_000019.9:g.847993C>T
ELANE RefSeqGene (LRG_57) NG_009627.1:g.703C>G
ELANE RefSeqGene (LRG_57) NG_009627.1:g.703C>T
GRCh38.p14 chr 19 alt locus HSCHR19_5_CTG2 NT_187622.1:g.26836C>G
GRCh38.p14 chr 19 alt locus HSCHR19_5_CTG2 NT_187622.1:g.26836C>T
Gene: PRTN3, proteinase 3 (plus strand)
Molecule type Change Amino acid[Codon] SO Term
PRTN3 transcript NM_002777.4:c.*24= N/A 3 Prime UTR Variant
PRTN3 transcript variant X1 XM_011528136.2:c.*223= N/A 3 Prime UTR 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 C= G T
GRCh38.p14 chr 19 NC_000019.10:g.847993= NC_000019.10:g.847993C>G NC_000019.10:g.847993C>T
GRCh37.p13 chr 19 NC_000019.9:g.847993= NC_000019.9:g.847993C>G NC_000019.9:g.847993C>T
ELANE RefSeqGene (LRG_57) NG_009627.1:g.703= NG_009627.1:g.703C>G NG_009627.1:g.703C>T
GRCh38.p14 chr 19 alt locus HSCHR19_5_CTG2 NT_187622.1:g.26836= NT_187622.1:g.26836C>G NT_187622.1:g.26836C>T
PRTN3 transcript NM_002777.4:c.*24= NM_002777.4:c.*24C>G NM_002777.4:c.*24C>T
PRTN3 transcript NM_002777.3:c.*24= NM_002777.3:c.*24C>G NM_002777.3:c.*24C>T
PRTN3 transcript variant X1 XM_011528136.2:c.*223= XM_011528136.2:c.*223C>G XM_011528136.2:c.*223C>T
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#.

37 SubSNP, 15 Frequency submissions
No Submitter Submission ID Date (Build)
1 SSAHASNP ss21556375 Apr 05, 2004 (121)
2 ABI ss44159005 Mar 13, 2006 (126)
3 HUMANGENOME_JCVI ss96284774 Feb 06, 2009 (130)
4 ENSEMBL ss132793916 Dec 01, 2009 (131)
5 1000GENOMES ss489139733 May 04, 2012 (137)
6 NHLBI-ESP ss713454165 Apr 25, 2013 (138)
7 EVA-GONL ss994002729 Aug 21, 2014 (142)
8 1000GENOMES ss1362025674 Aug 21, 2014 (142)
9 EVA_UK10K_ALSPAC ss1637415181 Apr 01, 2015 (144)
10 EVA_UK10K_TWINSUK ss1680409214 Apr 01, 2015 (144)
11 EVA_EXAC ss1693210300 Apr 01, 2015 (144)
12 EVA_DECODE ss1698065591 Apr 01, 2015 (144)
13 JJLAB ss2029515122 Sep 14, 2016 (149)
14 USC_VALOUEV ss2158025382 Dec 20, 2016 (150)
15 HUMAN_LONGEVITY ss2223627257 Dec 20, 2016 (150)
16 GNOMAD ss2743388540 Nov 08, 2017 (151)
17 GNOMAD ss2749989245 Nov 08, 2017 (151)
18 GNOMAD ss2959487537 Nov 08, 2017 (151)
19 SWEGEN ss3016944265 Nov 08, 2017 (151)
20 CSHL ss3352155819 Nov 08, 2017 (151)
21 URBANLAB ss3650850415 Oct 12, 2018 (152)
22 EGCUT_WGS ss3683794250 Jul 13, 2019 (153)
23 EVA_DECODE ss3702165661 Jul 13, 2019 (153)
24 ACPOP ss3742779054 Jul 13, 2019 (153)
25 EVA ss3825205724 Apr 27, 2020 (154)
26 EVA ss3825919313 Apr 27, 2020 (154)
27 SGDP_PRJ ss3887570153 Apr 27, 2020 (154)
28 TOPMED ss5065281852 Apr 26, 2021 (155)
29 TOPMED ss5065281853 Apr 26, 2021 (155)
30 1000G_HIGH_COVERAGE ss5306177606 Oct 16, 2022 (156)
31 EVA ss5433035682 Oct 16, 2022 (156)
32 HUGCELL_USP ss5498856042 Oct 16, 2022 (156)
33 1000G_HIGH_COVERAGE ss5611455155 Oct 16, 2022 (156)
34 EVA ss5840134153 Oct 16, 2022 (156)
35 EVA ss5848472491 Oct 16, 2022 (156)
36 EVA ss5926973114 Oct 16, 2022 (156)
37 EVA ss5953240518 Oct 16, 2022 (156)
38 1000Genomes NC_000019.9 - 847993 Oct 12, 2018 (152)
39 1000Genomes_30x NC_000019.10 - 847993 Oct 16, 2022 (156)
40 The Avon Longitudinal Study of Parents and Children NC_000019.9 - 847993 Oct 12, 2018 (152)
41 Genetic variation in the Estonian population NC_000019.9 - 847993 Oct 12, 2018 (152)
42 ExAC NC_000019.9 - 847993 Oct 12, 2018 (152)
43 gnomAD - Genomes NC_000019.10 - 847993 Apr 26, 2021 (155)
44 gnomAD - Exomes NC_000019.9 - 847993 Jul 13, 2019 (153)
45 GO Exome Sequencing Project NC_000019.9 - 847993 Oct 12, 2018 (152)
46 Northern Sweden NC_000019.9 - 847993 Jul 13, 2019 (153)
47 SGDP_PRJ NC_000019.9 - 847993 Apr 27, 2020 (154)
48 Siberian NC_000019.9 - 847993 Apr 27, 2020 (154)
49 TopMed

Submission ignored due to conflicting rows:
Row 280827516 (NC_000019.10:847992:C:G 1/264690)
Row 280827517 (NC_000019.10:847992:C:T 1128/264690)

- Apr 26, 2021 (155)
50 TopMed

Submission ignored due to conflicting rows:
Row 280827516 (NC_000019.10:847992:C:G 1/264690)
Row 280827517 (NC_000019.10:847992:C:T 1128/264690)

- Apr 26, 2021 (155)
51 UK 10K study - Twins NC_000019.9 - 847993 Oct 12, 2018 (152)
52 ALFA NC_000019.10 - 847993 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
3173456010, ss5065281852 NC_000019.10:847992:C:G NC_000019.10:847992:C:G (self)
ss1698065591 NC_000019.8:798992:C:T NC_000019.10:847992:C:T (self)
75390735, 41792304, 29532498, 3686402, 12702132, 1662730, 16063919, 39587133, 10541736, 41792304, ss489139733, ss713454165, ss994002729, ss1362025674, ss1637415181, ss1680409214, ss1693210300, ss2029515122, ss2158025382, ss2743388540, ss2749989245, ss2959487537, ss3016944265, ss3352155819, ss3683794250, ss3742779054, ss3825205724, ss3825919313, ss3887570153, ss5433035682, ss5840134153, ss5848472491, ss5953240518 NC_000019.9:847992:C:T NC_000019.10:847992:C:T (self)
98981090, 531654002, 3173456010, ss2223627257, ss3650850415, ss3702165661, ss5065281853, ss5306177606, ss5498856042, ss5611455155, ss5926973114 NC_000019.10:847992:C:T NC_000019.10:847992:C:T (self)
ss21556375, ss44159005, ss96284774, ss132793916 NT_011255.14:787992:C:T NC_000019.10:847992:C: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 rs12985970

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