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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.

rs919

Current Build 155

Released April 9, 2021

Organism
Homo sapiens
Position
chr18:12446690 (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>T
Variation Type
SNV Single Nucleotide Variation
Frequency
T=0.100393 (26573/264690, TOPMED)
T=0.101021 (14092/139496, GnomAD)
T=0.13231 (11860/89638, ALFA) (+ 16 more)
T=0.00012 (2/16758, 8.3KJPN)
T=0.0599 (300/5008, 1000G)
T=0.1042 (467/4480, Estonian)
T=0.1401 (540/3854, ALSPAC)
T=0.1340 (497/3708, TWINSUK)
T=0.0017 (5/2922, KOREAN)
T=0.0741 (126/1700, HapMap)
T=0.135 (135/998, GoNL)
T=0.128 (80/626, Chileans)
T=0.125 (75/600, NorthernSweden)
T=0.148 (32/216, Qatari)
T=0.009 (2/214, Vietnamese)
G=0.47 (32/68, SGDP_PRJ)
T=0.12 (5/40, GENOME_DK)
G=0.5 (2/4, Siberian)
T=0.5 (2/4, Siberian)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
SPIRE1 : 3 Prime UTR Variant
LOC105371998 : Intron 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 18 NC_000018.10:g.12446690G>T
GRCh37.p13 chr 18 NC_000018.9:g.12446689G>T
Gene: SPIRE1, spire type actin nucleation factor 1 (minus strand)
Molecule type Change Amino acid[Codon] SO Term
SPIRE1 transcript variant 3 NM_001128627.1:c.*2948= N/A 3 Prime UTR Variant
SPIRE1 transcript variant 1 NM_001128626.2:c.*2948= N/A 3 Prime UTR Variant
SPIRE1 transcript variant 2 NM_020148.3:c.*2948= N/A 3 Prime UTR Variant
SPIRE1 transcript variant X1 XM_011525701.1:c.*2948= N/A 3 Prime UTR Variant
SPIRE1 transcript variant X4 XM_011525702.1:c.*2948= N/A 3 Prime UTR Variant
SPIRE1 transcript variant X2 XM_005258122.4:c.*2948= N/A 3 Prime UTR Variant
SPIRE1 transcript variant X3 XM_024451224.1:c.*2948= N/A 3 Prime UTR Variant
SPIRE1 transcript variant X5 XM_024451225.1:c.*2948= N/A 3 Prime UTR Variant
SPIRE1 transcript variant X6 XM_011525703.2:c. N/A Genic Downstream Transcript Variant
Gene: LOC105371998, uncharacterized LOC105371998 (plus strand)
Molecule type Change Amino acid[Codon] SO Term
LOC105371998 transcript NR_136514.1: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

ALFA Allele Frequency (New)
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 89638 G=0.86769 T=0.13231
European Sub 75316 G=0.85374 T=0.14626
African Sub 4446 G=0.9694 T=0.0306
African Others Sub 178 G=0.994 T=0.006
African American Sub 4268 G=0.9684 T=0.0316
Asian Sub 3326 G=0.9913 T=0.0087
East Asian Sub 2666 G=0.9985 T=0.0015
Other Asian Sub 660 G=0.962 T=0.038
Latin American 1 Sub 590 G=0.851 T=0.149
Latin American 2 Sub 3086 G=0.8947 T=0.1053
South Asian Sub 286 G=0.944 T=0.056
Other Sub 2588 G=0.9034 T=0.0966


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=0.899607 T=0.100393
gnomAD - Genomes Global Study-wide 139496 G=0.898979 T=0.101021
gnomAD - Genomes European Sub 75814 G=0.86385 T=0.13615
gnomAD - Genomes African Sub 41542 G=0.97099 T=0.02901
gnomAD - Genomes American Sub 13562 G=0.87642 T=0.12358
gnomAD - Genomes Ashkenazi Jewish Sub 3318 G=0.8128 T=0.1872
gnomAD - Genomes East Asian Sub 3124 G=0.9965 T=0.0035
gnomAD - Genomes Other Sub 2136 G=0.8797 T=0.1203
8.3KJPN JAPANESE Study-wide 16758 G=0.99988 T=0.00012
1000Genomes Global Study-wide 5008 G=0.9401 T=0.0599
1000Genomes African Sub 1322 G=0.9856 T=0.0144
1000Genomes East Asian Sub 1008 G=0.9950 T=0.0050
1000Genomes Europe Sub 1006 G=0.8350 T=0.1650
1000Genomes South Asian Sub 978 G=0.957 T=0.043
1000Genomes American Sub 694 G=0.902 T=0.098
Genetic variation in the Estonian population Estonian Study-wide 4480 G=0.8958 T=0.1042
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 G=0.8599 T=0.1401
UK 10K study - Twins TWIN COHORT Study-wide 3708 G=0.8660 T=0.1340
KOREAN population from KRGDB KOREAN Study-wide 2922 G=0.9983 T=0.0017
HapMap Global Study-wide 1700 G=0.9259 T=0.0741
HapMap American Sub 770 G=0.929 T=0.071
HapMap African Sub 586 G=0.949 T=0.051
HapMap Europe Sub 176 G=0.773 T=0.227
HapMap Asian Sub 168 G=0.994 T=0.006
Genome of the Netherlands Release 5 Genome of the Netherlands Study-wide 998 G=0.865 T=0.135
Chileans Chilean Study-wide 626 G=0.872 T=0.128
Northern Sweden ACPOP Study-wide 600 G=0.875 T=0.125
Qatari Global Study-wide 216 G=0.852 T=0.148
A Vietnamese Genetic Variation Database Global Study-wide 214 G=0.991 T=0.009
SGDP_PRJ Global Study-wide 68 G=0.47 T=0.53
The Danish reference pan genome Danish Study-wide 40 G=0.88 T=0.12
Siberian Global Study-wide 4 G=0.5 T=0.5
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= T
GRCh38.p13 chr 18 NC_000018.10:g.12446690= NC_000018.10:g.12446690G>T
GRCh37.p13 chr 18 NC_000018.9:g.12446689= NC_000018.9:g.12446689G>T
SPIRE1 transcript variant X2 XM_005258122.4:c.*2948= XM_005258122.4:c.*2948C>A
SPIRE1 transcript variant X2 XM_005258122.1:c.*2948= XM_005258122.1:c.*2948C>A
SPIRE1 transcript variant 2 NM_020148.3:c.*2948= NM_020148.3:c.*2948C>A
SPIRE1 transcript variant 2 NM_020148.2:c.*2948= NM_020148.2:c.*2948C>A
SPIRE1 transcript variant 1 NM_001128626.2:c.*2948= NM_001128626.2:c.*2948C>A
SPIRE1 transcript variant 1 NM_001128626.1:c.*2948= NM_001128626.1:c.*2948C>A
SPIRE1 transcript variant X1 XM_011525701.1:c.*2948= XM_011525701.1:c.*2948C>A
SPIRE1 transcript variant X3 XM_024451224.1:c.*2948= XM_024451224.1:c.*2948C>A
SPIRE1 transcript variant X5 XM_024451225.1:c.*2948= XM_024451225.1:c.*2948C>A
SPIRE1 transcript variant X4 XM_011525702.1:c.*2948= XM_011525702.1:c.*2948C>A
SPIRE1 transcript variant 3 NM_001128627.1:c.*2948= NM_001128627.1:c.*2948C>A
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#.

49 SubSNP, 18 Frequency submissions
No Submitter Submission ID Date (Build)
1 WIAF ss942 Sep 19, 2000 (36)
2 LEE ss4408062 May 29, 2002 (106)
3 CGAP-GAI ss16248240 Feb 27, 2004 (120)
4 PERLEGEN ss69208249 May 17, 2007 (127)
5 AFFY ss74854407 Aug 16, 2007 (128)
6 AFFY ss76819148 Dec 08, 2007 (130)
7 KRIBB_YJKIM ss104807694 Feb 04, 2009 (130)
8 ENSEMBL ss143203003 Dec 01, 2009 (131)
9 1000GENOMES ss237388813 Jul 15, 2010 (132)
10 PJP ss292132565 May 09, 2011 (134)
11 ILLUMINA ss536312384 Sep 08, 2015 (146)
12 SSMP ss661337755 Apr 25, 2013 (138)
13 EVA-GONL ss993509586 Aug 21, 2014 (142)
14 JMKIDD_LAB ss1081343576 Aug 21, 2014 (142)
15 1000GENOMES ss1360189614 Aug 21, 2014 (142)
16 DDI ss1428152594 Apr 01, 2015 (144)
17 EVA_GENOME_DK ss1578318658 Apr 01, 2015 (144)
18 EVA_UK10K_ALSPAC ss1636440819 Apr 01, 2015 (144)
19 EVA_UK10K_TWINSUK ss1679434852 Apr 01, 2015 (144)
20 EVA_DECODE ss1697562506 Apr 01, 2015 (144)
21 EVA_SVP ss1713610954 Apr 01, 2015 (144)
22 WEILL_CORNELL_DGM ss1936981692 Feb 12, 2016 (147)
23 JJLAB ss2029263731 Sep 14, 2016 (149)
24 USC_VALOUEV ss2157759661 Dec 20, 2016 (150)
25 HUMAN_LONGEVITY ss2219928640 Dec 20, 2016 (150)
26 TOPMED ss2385187954 Dec 20, 2016 (150)
27 GNOMAD ss2954267719 Nov 08, 2017 (151)
28 SWEGEN ss3016181473 Nov 08, 2017 (151)
29 BIOINF_KMB_FNS_UNIBA ss3028459148 Nov 08, 2017 (151)
30 TOPMED ss3272884888 Nov 08, 2017 (151)
31 CSHL ss3351926749 Nov 08, 2017 (151)
32 ILLUMINA ss3627765066 Oct 12, 2018 (152)
33 OMUKHERJEE_ADBS ss3646520626 Oct 12, 2018 (152)
34 URBANLAB ss3650744437 Oct 12, 2018 (152)
35 EGCUT_WGS ss3683036899 Jul 13, 2019 (153)
36 EVA_DECODE ss3701249132 Jul 13, 2019 (153)
37 ACPOP ss3742367260 Jul 13, 2019 (153)
38 EVA ss3755138733 Jul 13, 2019 (153)
39 PACBIO ss3788317797 Jul 13, 2019 (153)
40 PACBIO ss3793257529 Jul 13, 2019 (153)
41 PACBIO ss3798143760 Jul 13, 2019 (153)
42 KHV_HUMAN_GENOMES ss3820404664 Jul 13, 2019 (153)
43 EVA ss3825913365 Apr 27, 2020 (154)
44 EVA ss3835069012 Apr 27, 2020 (154)
45 SGDP_PRJ ss3886582815 Apr 27, 2020 (154)
46 KRGDB ss3936392235 Apr 27, 2020 (154)
47 FSA-LAB ss3984130106 Apr 26, 2021 (155)
48 TOPMED ss5049187597 Apr 26, 2021 (155)
49 TOMMO_GENOMICS ss5224229822 Apr 26, 2021 (155)
50 1000Genomes NC_000018.9 - 12446689 Oct 12, 2018 (152)
51 The Avon Longitudinal Study of Parents and Children NC_000018.9 - 12446689 Oct 12, 2018 (152)
52 Chileans NC_000018.9 - 12446689 Apr 27, 2020 (154)
53 Genetic variation in the Estonian population NC_000018.9 - 12446689 Oct 12, 2018 (152)
54 The Danish reference pan genome NC_000018.9 - 12446689 Apr 27, 2020 (154)
55 gnomAD - Genomes NC_000018.10 - 12446690 Apr 26, 2021 (155)
56 Genome of the Netherlands Release 5 NC_000018.9 - 12446689 Apr 27, 2020 (154)
57 HapMap NC_000018.10 - 12446690 Apr 27, 2020 (154)
58 KOREAN population from KRGDB NC_000018.9 - 12446689 Apr 27, 2020 (154)
59 Northern Sweden NC_000018.9 - 12446689 Jul 13, 2019 (153)
60 Qatari NC_000018.9 - 12446689 Apr 27, 2020 (154)
61 SGDP_PRJ NC_000018.9 - 12446689 Apr 27, 2020 (154)
62 Siberian NC_000018.9 - 12446689 Apr 27, 2020 (154)
63 8.3KJPN NC_000018.9 - 12446689 Apr 26, 2021 (155)
64 TopMed NC_000018.10 - 12446690 Apr 26, 2021 (155)
65 UK 10K study - Twins NC_000018.9 - 12446689 Oct 12, 2018 (152)
66 A Vietnamese Genetic Variation Database NC_000018.9 - 12446689 Jul 13, 2019 (153)
67 ALFA NC_000018.10 - 12446690 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)
rs3185058 Jul 03, 2002 (106)
rs52810440 Sep 21, 2007 (128)
rs56537875 May 23, 2008 (130)
Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
ss292132565, ss1697562506, ss1713610954 NC_000018.8:12436688:G:T NC_000018.10:12446689:G:T (self)
73489519, 40721102, 190062, 28775147, 4514300, 18142916, 43569629, 15652125, 19023614, 38599795, 10276015, 82199129, 40721102, 9001598, ss237388813, ss536312384, ss661337755, ss993509586, ss1081343576, ss1360189614, ss1428152594, ss1578318658, ss1636440819, ss1679434852, ss1936981692, ss2029263731, ss2157759661, ss2385187954, ss2954267719, ss3016181473, ss3351926749, ss3627765066, ss3646520626, ss3683036899, ss3742367260, ss3755138733, ss3788317797, ss3793257529, ss3798143760, ss3825913365, ss3835069012, ss3886582815, ss3936392235, ss3984130106, ss5224229822 NC_000018.9:12446688:G:T NC_000018.10:12446689:G:T (self)
518401729, 1557569, 165200446, 264733260, 2676654679, ss2219928640, ss3028459148, ss3272884888, ss3650744437, ss3701249132, ss3820404664, ss5049187597 NC_000018.10:12446689:G:T NC_000018.10:12446689:G:T (self)
ss942, ss4408062, ss16248240, ss69208249, ss74854407, ss76819148, ss104807694, ss143203003 NT_010859.14:12436688:G:T NC_000018.10:12446689:G: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 rs919

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