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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.

rs12118976

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr1:26200819 (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
Variation Type
SNV Single Nucleotide Variation
Frequency
G=0.243968 (64576/264690, TOPMED)
G=0.199283 (49716/249474, GnomAD_exome)
G=0.256050 (35823/139906, GnomAD) (+ 20 more)
G=0.203462 (24568/120750, ExAC)
G=0.00294 (83/28258, 14KJPN)
G=0.24388 (6817/27952, ALFA)
G=0.00215 (36/16760, 8.3KJPN)
G=0.26065 (3390/13006, GO-ESP)
G=0.1991 (1275/6404, 1000G_30x)
G=0.1945 (974/5008, 1000G)
G=0.2475 (1109/4480, Estonian)
G=0.2299 (886/3854, ALSPAC)
G=0.2300 (853/3708, TWINSUK)
G=0.0062 (18/2920, KOREAN)
G=0.0104 (19/1832, Korea1K)
G=0.242 (242/998, GoNL)
G=0.218 (131/600, NorthernSweden)
G=0.133 (71/534, MGP)
G=0.211 (64/304, FINRISK)
G=0.199 (43/216, Qatari)
C=0.454 (59/130, SGDP_PRJ)
G=0.20 (8/40, GENOME_DK)
C=0.33 (4/12, Siberian)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
CATSPER4 : 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 27952 C=0.75612 G=0.24388
European Sub 20398 C=0.75963 G=0.24037
African Sub 3554 C=0.6849 G=0.3151
African Others Sub 122 C=0.664 G=0.336
African American Sub 3432 C=0.6856 G=0.3144
Asian Sub 168 C=0.964 G=0.036
East Asian Sub 112 C=0.955 G=0.045
Other Asian Sub 56 C=0.98 G=0.02
Latin American 1 Sub 146 C=0.747 G=0.253
Latin American 2 Sub 610 C=0.864 G=0.136
South Asian Sub 98 C=0.85 G=0.15
Other Sub 2978 C=0.7807 G=0.2193


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 C=0.756032 G=0.243968
gnomAD - Exomes Global Study-wide 249474 C=0.800717 G=0.199283
gnomAD - Exomes European Sub 133562 C=0.762417 G=0.237583
gnomAD - Exomes Asian Sub 48990 C=0.88826 G=0.11174
gnomAD - Exomes American Sub 34582 C=0.89127 G=0.10873
gnomAD - Exomes African Sub 16176 C=0.68262 G=0.31738
gnomAD - Exomes Ashkenazi Jewish Sub 10060 C=0.77207 G=0.22793
gnomAD - Exomes Other Sub 6104 C=0.7833 G=0.2167
gnomAD - Genomes Global Study-wide 139906 C=0.743950 G=0.256050
gnomAD - Genomes European Sub 75794 C=0.75452 G=0.24548
gnomAD - Genomes African Sub 41862 C=0.67758 G=0.32242
gnomAD - Genomes American Sub 13642 C=0.82510 G=0.17490
gnomAD - Genomes Ashkenazi Jewish Sub 3320 C=0.7759 G=0.2241
gnomAD - Genomes East Asian Sub 3134 C=0.9809 G=0.0191
gnomAD - Genomes Other Sub 2154 C=0.7539 G=0.2461
ExAC Global Study-wide 120750 C=0.796538 G=0.203462
ExAC Europe Sub 72862 C=0.76672 G=0.23328
ExAC Asian Sub 25142 C=0.88271 G=0.11729
ExAC American Sub 11564 C=0.89614 G=0.10386
ExAC African Sub 10284 C=0.68504 G=0.31496
ExAC Other Sub 898 C=0.797 G=0.203
14KJPN JAPANESE Study-wide 28258 C=0.99706 G=0.00294
Allele Frequency Aggregator Total Global 27952 C=0.75612 G=0.24388
Allele Frequency Aggregator European Sub 20398 C=0.75963 G=0.24037
Allele Frequency Aggregator African Sub 3554 C=0.6849 G=0.3151
Allele Frequency Aggregator Other Sub 2978 C=0.7807 G=0.2193
Allele Frequency Aggregator Latin American 2 Sub 610 C=0.864 G=0.136
Allele Frequency Aggregator Asian Sub 168 C=0.964 G=0.036
Allele Frequency Aggregator Latin American 1 Sub 146 C=0.747 G=0.253
Allele Frequency Aggregator South Asian Sub 98 C=0.85 G=0.15
8.3KJPN JAPANESE Study-wide 16760 C=0.99785 G=0.00215
GO Exome Sequencing Project Global Study-wide 13006 C=0.73935 G=0.26065
GO Exome Sequencing Project European American Sub 8600 C=0.7649 G=0.2351
GO Exome Sequencing Project African American Sub 4406 C=0.6895 G=0.3105
1000Genomes_30x Global Study-wide 6404 C=0.8009 G=0.1991
1000Genomes_30x African Sub 1786 C=0.6568 G=0.3432
1000Genomes_30x Europe Sub 1266 C=0.7630 G=0.2370
1000Genomes_30x South Asian Sub 1202 C=0.8478 G=0.1522
1000Genomes_30x East Asian Sub 1170 C=0.9769 G=0.0231
1000Genomes_30x American Sub 980 C=0.845 G=0.155
1000Genomes Global Study-wide 5008 C=0.8055 G=0.1945
1000Genomes African Sub 1322 C=0.6566 G=0.3434
1000Genomes East Asian Sub 1008 C=0.9782 G=0.0218
1000Genomes Europe Sub 1006 C=0.7545 G=0.2455
1000Genomes South Asian Sub 978 C=0.851 G=0.149
1000Genomes American Sub 694 C=0.849 G=0.151
Genetic variation in the Estonian population Estonian Study-wide 4480 C=0.7525 G=0.2475
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 C=0.7701 G=0.2299
UK 10K study - Twins TWIN COHORT Study-wide 3708 C=0.7700 G=0.2300
KOREAN population from KRGDB KOREAN Study-wide 2920 C=0.9938 G=0.0062
Korean Genome Project KOREAN Study-wide 1832 C=0.9896 G=0.0104
Genome of the Netherlands Release 5 Genome of the Netherlands Study-wide 998 C=0.758 G=0.242
Northern Sweden ACPOP Study-wide 600 C=0.782 G=0.218
Medical Genome Project healthy controls from Spanish population Spanish controls Study-wide 534 C=0.867 G=0.133
FINRISK Finnish from FINRISK project Study-wide 304 C=0.789 G=0.211
Qatari Global Study-wide 216 C=0.801 G=0.199
SGDP_PRJ Global Study-wide 130 C=0.454 G=0.546
The Danish reference pan genome Danish Study-wide 40 C=0.80 G=0.20
Siberian Global Study-wide 12 C=0.33 G=0.67
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.26200819C>G
GRCh37.p13 chr 1 NC_000001.10:g.26527310C>G
Gene: CATSPER4, cation channel sperm associated 4 (plus strand)
Molecule type Change Amino acid[Codon] SO Term
CATSPER4 transcript NM_198137.2:c.988-11C>G N/A Intron Variant
CATSPER4 transcript variant X1 XM_011541432.4:c.988-15C>G N/A Intron Variant
CATSPER4 transcript variant X2 XM_011541433.3: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 C= G
GRCh38.p14 chr 1 NC_000001.11:g.26200819= NC_000001.11:g.26200819C>G
GRCh37.p13 chr 1 NC_000001.10:g.26527310= NC_000001.10:g.26527310C>G
CATSPER4 transcript NM_198137.1:c.988-11= NM_198137.1:c.988-11C>G
CATSPER4 transcript NM_198137.2:c.988-11= NM_198137.2:c.988-11C>G
CATSPER4 transcript variant X1 XM_011541432.4:c.988-15= XM_011541432.4:c.988-15C>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#.

72 SubSNP, 23 Frequency submissions
No Submitter Submission ID Date (Build)
1 SC_SNP ss18247765 Feb 28, 2004 (120)
2 ILLUMINA-UK ss118577419 Feb 14, 2009 (130)
3 COMPLETE_GENOMICS ss166269729 Jul 04, 2010 (132)
4 BUSHMAN ss198199342 Jul 04, 2010 (132)
5 BCM-HGSC-SUB ss205398804 Jul 04, 2010 (132)
6 1000GENOMES ss218292798 Jul 14, 2010 (132)
7 1000GENOMES ss230468634 Jul 14, 2010 (132)
8 GMI ss284022400 Apr 25, 2013 (138)
9 1000GENOMES ss489729947 May 04, 2012 (137)
10 CLINSEQ_SNP ss491589575 May 04, 2012 (137)
11 ILLUMINA ss532910748 Sep 08, 2015 (146)
12 TISHKOFF ss553913490 Apr 25, 2013 (138)
13 SSMP ss647651566 Apr 25, 2013 (138)
14 NHLBI-ESP ss712289559 Apr 25, 2013 (138)
15 EVA-GONL ss974965936 Aug 21, 2014 (142)
16 JMKIDD_LAB ss1067418499 Aug 21, 2014 (142)
17 JMKIDD_LAB ss1067748115 Aug 21, 2014 (142)
18 1000GENOMES ss1290113498 Aug 21, 2014 (142)
19 DDI ss1425752372 Apr 01, 2015 (144)
20 EVA_GENOME_DK ss1573951716 Apr 01, 2015 (144)
21 EVA_FINRISK ss1584006138 Apr 01, 2015 (144)
22 EVA_UK10K_ALSPAC ss1599766674 Apr 01, 2015 (144)
23 EVA_UK10K_TWINSUK ss1642760707 Apr 01, 2015 (144)
24 EVA_EXAC ss1685405701 Apr 01, 2015 (144)
25 EVA_MGP ss1710896441 Apr 01, 2015 (144)
26 HAMMER_LAB ss1794089527 Sep 08, 2015 (146)
27 WEILL_CORNELL_DGM ss1918178214 Feb 12, 2016 (147)
28 JJLAB ss2019600745 Sep 14, 2016 (149)
29 USC_VALOUEV ss2147607092 Dec 20, 2016 (150)
30 HUMAN_LONGEVITY ss2160882435 Dec 20, 2016 (150)
31 GNOMAD ss2731275267 Nov 08, 2017 (151)
32 GNOMAD ss2746265336 Nov 08, 2017 (151)
33 GNOMAD ss2752894004 Nov 08, 2017 (151)
34 SWEGEN ss2986498283 Nov 08, 2017 (151)
35 BIOINF_KMB_FNS_UNIBA ss3023565937 Nov 08, 2017 (151)
36 CSHL ss3343375440 Nov 08, 2017 (151)
37 ILLUMINA ss3626053259 Oct 11, 2018 (152)
38 OMUKHERJEE_ADBS ss3646227438 Oct 11, 2018 (152)
39 EGCUT_WGS ss3654563574 Jul 12, 2019 (153)
40 ACPOP ss3726885014 Jul 12, 2019 (153)
41 EVA ss3745963860 Jul 12, 2019 (153)
42 PACBIO ss3783359123 Jul 12, 2019 (153)
43 PACBIO ss3789027689 Jul 12, 2019 (153)
44 PACBIO ss3793900193 Jul 12, 2019 (153)
45 KHV_HUMAN_GENOMES ss3798984486 Jul 12, 2019 (153)
46 EVA ss3823581351 Apr 25, 2020 (154)
47 EVA ss3826081066 Apr 25, 2020 (154)
48 SGDP_PRJ ss3848451106 Apr 25, 2020 (154)
49 KRGDB ss3893372704 Apr 25, 2020 (154)
50 KOGIC ss3944080046 Apr 25, 2020 (154)
51 FSA-LAB ss3983923904 Apr 27, 2021 (155)
52 EVA ss3986108731 Apr 27, 2021 (155)
53 TOPMED ss4442812745 Apr 27, 2021 (155)
54 TOMMO_GENOMICS ss5143024335 Apr 27, 2021 (155)
55 EVA ss5237160630 Apr 27, 2021 (155)
56 EVA ss5237631518 Oct 13, 2022 (156)
57 1000G_HIGH_COVERAGE ss5241579551 Oct 13, 2022 (156)
58 EVA ss5317463098 Oct 13, 2022 (156)
59 HUGCELL_USP ss5442721471 Oct 13, 2022 (156)
60 EVA ss5505794414 Oct 13, 2022 (156)
61 1000G_HIGH_COVERAGE ss5513521379 Oct 13, 2022 (156)
62 EVA ss5623913645 Oct 13, 2022 (156)
63 EVA ss5623990170 Oct 13, 2022 (156)
64 SANFORD_IMAGENETICS ss5625151109 Oct 13, 2022 (156)
65 TOMMO_GENOMICS ss5667495624 Oct 13, 2022 (156)
66 EVA ss5800079802 Oct 13, 2022 (156)
67 YY_MCH ss5800429163 Oct 13, 2022 (156)
68 EVA ss5831696446 Oct 13, 2022 (156)
69 EVA ss5848253855 Oct 13, 2022 (156)
70 EVA ss5848830336 Oct 13, 2022 (156)
71 EVA ss5907475311 Oct 13, 2022 (156)
72 EVA ss5936967604 Oct 13, 2022 (156)
73 1000Genomes NC_000001.10 - 26527310 Oct 11, 2018 (152)
74 1000Genomes_30x NC_000001.11 - 26200819 Oct 13, 2022 (156)
75 The Avon Longitudinal Study of Parents and Children NC_000001.10 - 26527310 Oct 11, 2018 (152)
76 Genetic variation in the Estonian population NC_000001.10 - 26527310 Oct 11, 2018 (152)
77 ExAC NC_000001.10 - 26527310 Oct 11, 2018 (152)
78 FINRISK NC_000001.10 - 26527310 Apr 25, 2020 (154)
79 The Danish reference pan genome NC_000001.10 - 26527310 Apr 25, 2020 (154)
80 gnomAD - Genomes NC_000001.11 - 26200819 Apr 27, 2021 (155)
81 gnomAD - Exomes NC_000001.10 - 26527310 Jul 12, 2019 (153)
82 GO Exome Sequencing Project NC_000001.10 - 26527310 Oct 11, 2018 (152)
83 Genome of the Netherlands Release 5 NC_000001.10 - 26527310 Apr 25, 2020 (154)
84 KOREAN population from KRGDB NC_000001.10 - 26527310 Apr 25, 2020 (154)
85 Korean Genome Project NC_000001.11 - 26200819 Apr 25, 2020 (154)
86 Medical Genome Project healthy controls from Spanish population NC_000001.10 - 26527310 Apr 25, 2020 (154)
87 Northern Sweden NC_000001.10 - 26527310 Jul 12, 2019 (153)
88 Qatari NC_000001.10 - 26527310 Apr 25, 2020 (154)
89 SGDP_PRJ NC_000001.10 - 26527310 Apr 25, 2020 (154)
90 Siberian NC_000001.10 - 26527310 Apr 25, 2020 (154)
91 8.3KJPN NC_000001.10 - 26527310 Apr 27, 2021 (155)
92 14KJPN NC_000001.11 - 26200819 Oct 13, 2022 (156)
93 TopMed NC_000001.11 - 26200819 Apr 27, 2021 (155)
94 UK 10K study - Twins NC_000001.10 - 26527310 Oct 11, 2018 (152)
95 ALFA NC_000001.11 - 26200819 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
ss118577419, ss166269729, ss198199342, ss205398804, ss284022400, ss491589575 NC_000001.9:26399896:C:G NC_000001.11:26200818:C:G (self)
804298, 427983, 301822, 4591920, 2599, 1432672, 289549, 40048, 185063, 550098, 13193, 169879, 220144, 468086, 123446, 993642, 427983, ss218292798, ss230468634, ss489729947, ss532910748, ss553913490, ss647651566, ss712289559, ss974965936, ss1067418499, ss1067748115, ss1290113498, ss1425752372, ss1573951716, ss1584006138, ss1599766674, ss1642760707, ss1685405701, ss1710896441, ss1794089527, ss1918178214, ss2019600745, ss2147607092, ss2731275267, ss2746265336, ss2752894004, ss2986498283, ss3343375440, ss3626053259, ss3646227438, ss3654563574, ss3726885014, ss3745963860, ss3783359123, ss3789027689, ss3793900193, ss3823581351, ss3826081066, ss3848451106, ss3893372704, ss3983923904, ss3986108731, ss5143024335, ss5317463098, ss5505794414, ss5623913645, ss5623990170, ss5625151109, ss5800079802, ss5831696446, ss5848253855, ss5936967604 NC_000001.10:26527309:C:G NC_000001.11:26200818:C:G (self)
1047314, 5625252, 458047, 1332728, 6419080, 951918837, ss2160882435, ss3023565937, ss3798984486, ss3944080046, ss4442812745, ss5237160630, ss5237631518, ss5241579551, ss5442721471, ss5513521379, ss5667495624, ss5800429163, ss5848830336, ss5907475311 NC_000001.11:26200818:C:G NC_000001.11:26200818:C:G (self)
ss18247765 NT_037485.3:638518:C:G NC_000001.11:26200818:C: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 rs12118976

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