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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.

rs12172719

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr1:42614230 (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
G>A
Variation Type
SNV Single Nucleotide Variation
Frequency
A=0.126083 (33373/264690, TOPMED)
A=0.118940 (16579/139390, GnomAD)
A=0.26138 (7384/28250, 14KJPN) (+ 13 more)
A=0.11598 (2148/18520, ALFA)
A=0.25952 (4349/16758, 8.3KJPN)
A=0.1788 (1145/6404, 1000G_30x)
A=0.1843 (923/5008, 1000G)
A=0.0797 (357/4480, Estonian)
A=0.2222 (651/2930, KOREAN)
A=0.118 (71/600, NorthernSweden)
A=0.153 (33/216, Qatari)
G=0.429 (91/212, SGDP_PRJ)
A=0.358 (76/212, Vietnamese)
A=0.15 (6/40, GENOME_DK)
G=0.5 (3/6, Siberian)
A=0.5 (3/6, Siberian)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
CCDC30 : Intron Variant
LOC124904162 : 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 18520 G=0.88402 A=0.11598
European Sub 14152 G=0.88694 A=0.11306
African Sub 2898 G=0.8844 A=0.1156
African Others Sub 114 G=0.860 A=0.140
African American Sub 2784 G=0.8854 A=0.1146
Asian Sub 112 G=0.732 A=0.268
East Asian Sub 86 G=0.78 A=0.22
Other Asian Sub 26 G=0.58 A=0.42
Latin American 1 Sub 146 G=0.884 A=0.116
Latin American 2 Sub 610 G=0.889 A=0.111
South Asian Sub 98 G=0.66 A=0.34
Other Sub 504 G=0.871 A=0.129


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=0.873917 A=0.126083
gnomAD - Genomes Global Study-wide 139390 G=0.881060 A=0.118940
gnomAD - Genomes European Sub 75572 G=0.87843 A=0.12157
gnomAD - Genomes African Sub 41700 G=0.89477 A=0.10523
gnomAD - Genomes American Sub 13560 G=0.89100 A=0.10900
gnomAD - Genomes Ashkenazi Jewish Sub 3314 G=0.8847 A=0.1153
gnomAD - Genomes East Asian Sub 3110 G=0.7190 A=0.2810
gnomAD - Genomes Other Sub 2134 G=0.8735 A=0.1265
14KJPN JAPANESE Study-wide 28250 G=0.73862 A=0.26138
Allele Frequency Aggregator Total Global 18520 G=0.88402 A=0.11598
Allele Frequency Aggregator European Sub 14152 G=0.88694 A=0.11306
Allele Frequency Aggregator African Sub 2898 G=0.8844 A=0.1156
Allele Frequency Aggregator Latin American 2 Sub 610 G=0.889 A=0.111
Allele Frequency Aggregator Other Sub 504 G=0.871 A=0.129
Allele Frequency Aggregator Latin American 1 Sub 146 G=0.884 A=0.116
Allele Frequency Aggregator Asian Sub 112 G=0.732 A=0.268
Allele Frequency Aggregator South Asian Sub 98 G=0.66 A=0.34
8.3KJPN JAPANESE Study-wide 16758 G=0.74048 A=0.25952
1000Genomes_30x Global Study-wide 6404 G=0.8212 A=0.1788
1000Genomes_30x African Sub 1786 G=0.9087 A=0.0913
1000Genomes_30x Europe Sub 1266 G=0.8618 A=0.1382
1000Genomes_30x South Asian Sub 1202 G=0.7047 A=0.2953
1000Genomes_30x East Asian Sub 1170 G=0.7000 A=0.3000
1000Genomes_30x American Sub 980 G=0.897 A=0.103
1000Genomes Global Study-wide 5008 G=0.8157 A=0.1843
1000Genomes African Sub 1322 G=0.9039 A=0.0961
1000Genomes East Asian Sub 1008 G=0.7063 A=0.2937
1000Genomes Europe Sub 1006 G=0.8678 A=0.1322
1000Genomes South Asian Sub 978 G=0.702 A=0.298
1000Genomes American Sub 694 G=0.890 A=0.110
Genetic variation in the Estonian population Estonian Study-wide 4480 G=0.9203 A=0.0797
KOREAN population from KRGDB KOREAN Study-wide 2930 G=0.7778 A=0.2222
Northern Sweden ACPOP Study-wide 600 G=0.882 A=0.118
Qatari Global Study-wide 216 G=0.847 A=0.153
SGDP_PRJ Global Study-wide 212 G=0.429 A=0.571
A Vietnamese Genetic Variation Database Global Study-wide 212 G=0.642 A=0.358
The Danish reference pan genome Danish Study-wide 40 G=0.85 A=0.15
Siberian Global Study-wide 6 G=0.5 A=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 1 NC_000001.11:g.42614230G>A
GRCh37.p13 chr 1 NC_000001.10:g.43079901G>A
Gene: CCDC30, coiled-coil domain containing 30 (plus strand)
Molecule type Change Amino acid[Codon] SO Term
CCDC30 transcript variant 1 NM_001080850.4:c.1496+314…

NM_001080850.4:c.1496+3140G>A

N/A Intron Variant
CCDC30 transcript variant 2 NM_001355224.2:c.590+3140…

NM_001355224.2:c.590+3140G>A

N/A Intron Variant
CCDC30 transcript variant 3 NM_001355226.2:c.590+3140…

NM_001355226.2:c.590+3140G>A

N/A Intron Variant
CCDC30 transcript variant 4 NM_001355227.2:c.590+3140…

NM_001355227.2:c.590+3140G>A

N/A Intron Variant
CCDC30 transcript variant 5 NM_001395379.1:c.1403+314…

NM_001395379.1:c.1403+3140G>A

N/A Intron Variant
CCDC30 transcript variant 6 NM_001395382.1:c.1277+314…

NM_001395382.1:c.1277+3140G>A

N/A Intron Variant
CCDC30 transcript variant 7 NM_001395383.1:c.1277+314…

NM_001395383.1:c.1277+3140G>A

N/A Intron Variant
CCDC30 transcript variant 8 NM_001395384.1:c.1277+314…

NM_001395384.1:c.1277+3140G>A

N/A Intron Variant
CCDC30 transcript variant 9 NM_001395385.1:c.1277+314…

NM_001395385.1:c.1277+3140G>A

N/A Intron Variant
CCDC30 transcript variant 10 NM_001395517.1:c.1961+314…

NM_001395517.1:c.1961+3140G>A

N/A Intron Variant
CCDC30 transcript variant X1 XM_047429779.1:c.1277+314…

XM_047429779.1:c.1277+3140G>A

N/A Intron Variant
Gene: LOC124904162, uncharacterized LOC124904162 (minus strand)
Molecule type Change Amino acid[Codon] SO Term
LOC124904162 transcript variant X2 XR_007066034.1:n. N/A Intron Variant
LOC124904162 transcript variant X1 XR_007066033.1:n. 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 G= A
GRCh38.p14 chr 1 NC_000001.11:g.42614230= NC_000001.11:g.42614230G>A
GRCh37.p13 chr 1 NC_000001.10:g.43079901= NC_000001.10:g.43079901G>A
CCDC30 transcript NM_001080850.2:c.1496+3140= NM_001080850.2:c.1496+3140G>A
CCDC30 transcript variant 1 NM_001080850.4:c.1496+3140= NM_001080850.4:c.1496+3140G>A
CCDC30 transcript variant 2 NM_001355224.2:c.590+3140= NM_001355224.2:c.590+3140G>A
CCDC30 transcript variant 3 NM_001355226.2:c.590+3140= NM_001355226.2:c.590+3140G>A
CCDC30 transcript variant 4 NM_001355227.2:c.590+3140= NM_001355227.2:c.590+3140G>A
CCDC30 transcript variant 5 NM_001395379.1:c.1403+3140= NM_001395379.1:c.1403+3140G>A
CCDC30 transcript variant 6 NM_001395382.1:c.1277+3140= NM_001395382.1:c.1277+3140G>A
CCDC30 transcript variant 7 NM_001395383.1:c.1277+3140= NM_001395383.1:c.1277+3140G>A
CCDC30 transcript variant 8 NM_001395384.1:c.1277+3140= NM_001395384.1:c.1277+3140G>A
CCDC30 transcript variant 9 NM_001395385.1:c.1277+3140= NM_001395385.1:c.1277+3140G>A
CCDC30 transcript variant 10 NM_001395517.1:c.1961+3140= NM_001395517.1:c.1961+3140G>A
CCDC30 transcript variant X1 XM_005271165.1:c.1496+3140= XM_005271165.1:c.1496+3140G>A
CCDC30 transcript variant X1 XM_047429779.1:c.1277+3140= XM_047429779.1:c.1277+3140G>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#.

40 SubSNP, 15 Frequency submissions
No Submitter Submission ID Date (Build)
1 SC_SNP ss18339035 Feb 28, 2004 (120)
2 COMPLETE_GENOMICS ss164174813 Jul 04, 2010 (132)
3 COMPLETE_GENOMICS ss166429591 Jul 04, 2010 (132)
4 1000GENOMES ss328560963 May 09, 2011 (134)
5 TISHKOFF ss554035744 Apr 25, 2013 (138)
6 SSMP ss647822364 Apr 25, 2013 (138)
7 EVA-GONL ss975080304 Aug 21, 2014 (142)
8 1000GENOMES ss1290564886 Aug 21, 2014 (142)
9 DDI ss1425785061 Apr 01, 2015 (144)
10 EVA_GENOME_DK ss1574015471 Apr 01, 2015 (144)
11 WEILL_CORNELL_DGM ss1918288722 Feb 12, 2016 (147)
12 JJLAB ss2019659270 Sep 14, 2016 (149)
13 USC_VALOUEV ss2147670696 Dec 20, 2016 (150)
14 HUMAN_LONGEVITY ss2161822959 Dec 20, 2016 (150)
15 SYSTEMSBIOZJU ss2624345099 Nov 08, 2017 (151)
16 GRF ss2697580003 Nov 08, 2017 (151)
17 GNOMAD ss2754200908 Nov 08, 2017 (151)
18 SWEGEN ss2986683588 Nov 08, 2017 (151)
19 CSHL ss3343421817 Nov 08, 2017 (151)
20 EGCUT_WGS ss3654749168 Jul 12, 2019 (153)
21 EVA_DECODE ss3686612717 Jul 12, 2019 (153)
22 ACPOP ss3726979474 Jul 12, 2019 (153)
23 EVA ss3746102793 Jul 12, 2019 (153)
24 KHV_HUMAN_GENOMES ss3799116360 Jul 12, 2019 (153)
25 EVA ss3826134480 Apr 25, 2020 (154)
26 SGDP_PRJ ss3848680894 Apr 25, 2020 (154)
27 KRGDB ss3893655122 Apr 25, 2020 (154)
28 TOPMED ss4446780761 Apr 25, 2021 (155)
29 TOMMO_GENOMICS ss5143562416 Apr 25, 2021 (155)
30 1000G_HIGH_COVERAGE ss5241983050 Oct 17, 2022 (156)
31 EVA ss5318199788 Oct 17, 2022 (156)
32 HUGCELL_USP ss5443078673 Oct 17, 2022 (156)
33 EVA ss5505824493 Oct 17, 2022 (156)
34 1000G_HIGH_COVERAGE ss5514115375 Oct 17, 2022 (156)
35 SANFORD_IMAGENETICS ss5625371059 Oct 17, 2022 (156)
36 TOMMO_GENOMICS ss5668212079 Oct 17, 2022 (156)
37 YY_MCH ss5800525421 Oct 17, 2022 (156)
38 EVA ss5831850856 Oct 17, 2022 (156)
39 EVA ss5907931053 Oct 17, 2022 (156)
40 EVA ss5937195142 Oct 17, 2022 (156)
41 1000Genomes NC_000001.10 - 43079901 Oct 11, 2018 (152)
42 1000Genomes_30x NC_000001.11 - 42614230 Oct 17, 2022 (156)
43 Genetic variation in the Estonian population NC_000001.10 - 43079901 Oct 11, 2018 (152)
44 The Danish reference pan genome NC_000001.10 - 43079901 Apr 25, 2020 (154)
45 gnomAD - Genomes NC_000001.11 - 42614230 Apr 25, 2021 (155)
46 KOREAN population from KRGDB NC_000001.10 - 43079901 Apr 25, 2020 (154)
47 Northern Sweden NC_000001.10 - 43079901 Jul 12, 2019 (153)
48 Qatari NC_000001.10 - 43079901 Apr 25, 2020 (154)
49 SGDP_PRJ NC_000001.10 - 43079901 Apr 25, 2020 (154)
50 Siberian NC_000001.10 - 43079901 Apr 25, 2020 (154)
51 8.3KJPN NC_000001.10 - 43079901 Apr 25, 2021 (155)
52 14KJPN NC_000001.11 - 42614230 Oct 17, 2022 (156)
53 TopMed NC_000001.11 - 42614230 Apr 25, 2021 (155)
54 A Vietnamese Genetic Variation Database NC_000001.10 - 43079901 Jul 12, 2019 (153)
55 ALFA NC_000001.11 - 42614230 Apr 25, 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
ss164174813, ss166429591 NC_000001.9:42852487:G:A NC_000001.11:42614229:G:A (self)
1271672, 487416, 1473471, 832516, 264339, 330652, 697874, 187050, 1531723, 141928, ss328560963, ss554035744, ss647822364, ss975080304, ss1290564886, ss1425785061, ss1574015471, ss1918288722, ss2019659270, ss2147670696, ss2624345099, ss2697580003, ss2754200908, ss2986683588, ss3343421817, ss3654749168, ss3726979474, ss3746102793, ss3826134480, ss3848680894, ss3893655122, ss5143562416, ss5318199788, ss5505824493, ss5625371059, ss5831850856, ss5937195142 NC_000001.10:43079900:G:A NC_000001.11:42614229:G:A (self)
1641310, 8957997, 2049183, 10387096, 9775799891, ss2161822959, ss3686612717, ss3799116360, ss4446780761, ss5241983050, ss5443078673, ss5514115375, ss5668212079, ss5800525421, ss5907931053 NC_000001.11:42614229:G:A NC_000001.11:42614229:G:A (self)
ss18339035 NT_032977.9:13051818:G:A NC_000001.11:42614229:G:A (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 rs12172719

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