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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.

rs12021508

Current Build 155

Released April 9, 2021

Organism
Homo sapiens
Position
chr1:155927524 (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>C
Variation Type
SNV Single Nucleotide Variation
Frequency
C=0.004126 (1092/264690, TOPMED)
C=0.002069 (290/140154, GnomAD)
C=0.05555 (931/16760, 8.3KJPN) (+ 10 more)
C=0.00135 (21/15598, ALFA)
C=0.0090 (45/5008, 1000G)
C=0.0003 (1/3854, ALSPAC)
C=0.0000 (0/3708, TWINSUK)
C=0.0676 (198/2930, KOREAN)
C=0.0671 (123/1832, Korea1K)
C=0.006 (2/324, HapMap)
C=0.023 (5/214, Vietnamese)
G=0.50 (10/20, SGDP_PRJ)
C=0.50 (10/20, SGDP_PRJ)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
KHDC4 : Intron Variant
SCARNA4 : 2KB Upstream 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 1 NC_000001.11:g.155927524G>C
GRCh37.p13 chr 1 NC_000001.10:g.155897315G>C
Gene: KHDC4, KH domain containing 4, pre-mRNA splicing factor (minus strand)
Molecule type Change Amino acid[Codon] SO Term
KHDC4 transcript NM_014949.4:c.465-368C>G N/A Intron Variant
Gene: SCARNA4, small Cajal body-specific RNA 4 (minus strand) : 2KB Upstream Variant
Molecule type Change Amino acid[Codon] SO Term
SCARNA4 transcript NR_003005.1:n. N/A Upstream 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

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: 20201027095038
Population Group Sample Size Ref Allele Alt Allele
Total Global 15598 G=0.99865 C=0.00135
European Sub 10974 G=0.99964 C=0.00036
African Sub 2946 G=0.9993 C=0.0007
African Others Sub 114 G=1.000 C=0.000
African American Sub 2832 G=0.9993 C=0.0007
Asian Sub 112 G=0.973 C=0.027
East Asian Sub 86 G=0.98 C=0.02
Other Asian Sub 26 G=0.96 C=0.04
Latin American 1 Sub 146 G=1.000 C=0.000
Latin American 2 Sub 610 G=0.989 C=0.011
South Asian Sub 98 G=1.00 C=0.00
Other Sub 712 G=0.993 C=0.007


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=0.995874 C=0.004126
gnomAD - Genomes Global Study-wide 140154 G=0.997931 C=0.002069
gnomAD - Genomes European Sub 75934 G=0.99971 C=0.00029
gnomAD - Genomes African Sub 41990 G=0.99969 C=0.00031
gnomAD - Genomes American Sub 13632 G=0.99325 C=0.00675
gnomAD - Genomes Ashkenazi Jewish Sub 3322 G=0.9985 C=0.0015
gnomAD - Genomes East Asian Sub 3126 G=0.9514 C=0.0486
gnomAD - Genomes Other Sub 2150 G=0.9972 C=0.0028
8.3KJPN JAPANESE Study-wide 16760 G=0.94445 C=0.05555
1000Genomes Global Study-wide 5008 G=0.9910 C=0.0090
1000Genomes African Sub 1322 G=1.0000 C=0.0000
1000Genomes East Asian Sub 1008 G=0.9623 C=0.0377
1000Genomes Europe Sub 1006 G=1.0000 C=0.0000
1000Genomes South Asian Sub 978 G=0.999 C=0.001
1000Genomes American Sub 694 G=0.991 C=0.009
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 G=0.9997 C=0.0003
UK 10K study - Twins TWIN COHORT Study-wide 3708 G=1.0000 C=0.0000
KOREAN population from KRGDB KOREAN Study-wide 2930 G=0.9324 C=0.0676
Korean Genome Project KOREAN Study-wide 1832 G=0.9329 C=0.0671
HapMap Global Study-wide 324 G=0.994 C=0.006
HapMap African Sub 120 G=1.000 C=0.000
HapMap American Sub 120 G=1.000 C=0.000
HapMap Asian Sub 84 G=0.98 C=0.02
A Vietnamese Genetic Variation Database Global Study-wide 214 G=0.977 C=0.023
SGDP_PRJ Global Study-wide 20 G=0.50 C=0.50
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= C
GRCh38.p13 chr 1 NC_000001.11:g.155927524= NC_000001.11:g.155927524G>C
GRCh37.p13 chr 1 NC_000001.10:g.155897315= NC_000001.10:g.155897315G>C
KIAA0907 transcript NM_014949.2:c.465-368= NM_014949.2:c.465-368C>G
KHDC4 transcript NM_014949.4:c.465-368= NM_014949.4:c.465-368C>G
KIAA0907 transcript variant X1 XM_005244969.1:c.465-368= XM_005244969.1:c.465-368C>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#.

28 SubSNP, 12 Frequency submissions
No Submitter Submission ID Date (Build)
1 SC_SNP ss18069722 Feb 28, 2004 (120)
2 GMI ss155761849 Dec 01, 2009 (131)
3 ILLUMINA ss160026516 Dec 01, 2009 (131)
4 1000GENOMES ss238381363 Jul 15, 2010 (132)
5 GMI ss276053511 May 04, 2012 (137)
6 ILLUMINA ss480171903 Sep 08, 2015 (146)
7 SSMP ss648418623 Apr 25, 2013 (138)
8 JMKIDD_LAB ss1068274164 Aug 21, 2014 (142)
9 1000GENOMES ss1292958964 Aug 21, 2014 (142)
10 EVA_UK10K_ALSPAC ss1601230816 Apr 01, 2015 (144)
11 EVA_UK10K_TWINSUK ss1644224849 Apr 01, 2015 (144)
12 GENOMED ss1966868740 Jul 19, 2016 (147)
13 JJLAB ss2019977101 Sep 14, 2016 (149)
14 HUMAN_LONGEVITY ss2166611167 Dec 20, 2016 (150)
15 TOPMED ss2329120938 Dec 20, 2016 (150)
16 GRF ss2697975154 Nov 08, 2017 (151)
17 GNOMAD ss2761421556 Nov 08, 2017 (151)
18 SWEGEN ss2987766242 Nov 08, 2017 (151)
19 TOPMED ss3092388748 Nov 08, 2017 (151)
20 ILLUMINA ss3636029950 Oct 11, 2018 (152)
21 EVA_DECODE ss3687799202 Jul 12, 2019 (153)
22 EVA ss3746817449 Jul 12, 2019 (153)
23 KHV_HUMAN_GENOMES ss3799817753 Jul 12, 2019 (153)
24 SGDP_PRJ ss3850022426 Apr 25, 2020 (154)
25 KRGDB ss3895235793 Apr 25, 2020 (154)
26 KOGIC ss3945670234 Apr 25, 2020 (154)
27 TOPMED ss4468624438 Apr 25, 2021 (155)
28 TOMMO_GENOMICS ss5146527379 Apr 25, 2021 (155)
29 1000Genomes NC_000001.10 - 155897315 Oct 11, 2018 (152)
30 The Avon Longitudinal Study of Parents and Children NC_000001.10 - 155897315 Oct 11, 2018 (152)
31 gnomAD - Genomes NC_000001.11 - 155927524 Apr 25, 2021 (155)
32 HapMap NC_000001.11 - 155927524 Apr 25, 2020 (154)
33 KOREAN population from KRGDB NC_000001.10 - 155897315 Apr 25, 2020 (154)
34 Korean Genome Project NC_000001.11 - 155927524 Apr 25, 2020 (154)
35 SGDP_PRJ NC_000001.10 - 155897315 Apr 25, 2020 (154)
36 8.3KJPN NC_000001.10 - 155897315 Apr 25, 2021 (155)
37 TopMed NC_000001.11 - 155927524 Apr 25, 2021 (155)
38 UK 10K study - Twins NC_000001.10 - 155897315 Oct 11, 2018 (152)
39 A Vietnamese Genetic Variation Database NC_000001.10 - 155897315 Jul 12, 2019 (153)
40 ALFA NC_000001.11 - 155927524 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
ss276053511 NC_000001.9:154163938:G:C NC_000001.11:155927523:G:C (self)
3752181, 2039921, 2413187, 2039406, 4496686, 2039921, 437311, ss238381363, ss480171903, ss648418623, ss1068274164, ss1292958964, ss1601230816, ss1644224849, ss1966868740, ss2019977101, ss2329120938, ss2697975154, ss2761421556, ss2987766242, ss3636029950, ss3746817449, ss3850022426, ss3895235793, ss5146527379 NC_000001.10:155897314:G:C NC_000001.11:155927523:G:C (self)
27322702, 177770, 2048235, 20233609, 32230773, 6171415224, ss2166611167, ss3092388748, ss3687799202, ss3799817753, ss3945670234, ss4468624438 NC_000001.11:155927523:G:C NC_000001.11:155927523:G:C (self)
ss155761849, ss160026516 NT_004487.19:7385956:G:C NC_000001.11:155927523:G:C (self)
ss18069722 NT_079484.1:2347146:G:C NC_000001.11:155927523:G:C (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 rs12021508

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