Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation

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.

rs576598349

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr11:66026217 (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=0.000036 (9/250944, GnomAD_exome)
T=0.000041 (5/121252, ExAC)
G=0.00000 (0/11862, ALFA) (+ 3 more)
T=0.00000 (0/11862, ALFA)
T=0.0005 (3/6404, 1000G_30x)
T=0.0004 (2/5008, 1000G)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
CATSPER1 : Missense 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 11862 C=1.00000 G=0.00000, T=0.00000
European Sub 7618 C=1.0000 G=0.0000, T=0.0000
African Sub 2816 C=1.0000 G=0.0000, T=0.0000
African Others Sub 108 C=1.000 G=0.000, T=0.000
African American Sub 2708 C=1.0000 G=0.0000, T=0.0000
Asian Sub 108 C=1.000 G=0.000, T=0.000
East Asian Sub 84 C=1.00 G=0.00, T=0.00
Other Asian Sub 24 C=1.00 G=0.00, T=0.00
Latin American 1 Sub 146 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 94 C=1.00 G=0.00, T=0.00
Other Sub 470 C=1.000 G=0.000, T=0.000


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 250944 C=0.999964 T=0.000036
gnomAD - Exomes European Sub 135022 C=1.000000 T=0.000000
gnomAD - Exomes Asian Sub 48962 C=0.99982 T=0.00018
gnomAD - Exomes American Sub 34558 C=1.00000 T=0.00000
gnomAD - Exomes African Sub 16254 C=1.00000 T=0.00000
gnomAD - Exomes Ashkenazi Jewish Sub 10030 C=1.00000 T=0.00000
gnomAD - Exomes Other Sub 6118 C=1.0000 T=0.0000
ExAC Global Study-wide 121252 C=0.999959 T=0.000041
ExAC Europe Sub 73280 C=1.00000 T=0.00000
ExAC Asian Sub 25082 C=0.99980 T=0.00020
ExAC American Sub 11578 C=1.00000 T=0.00000
ExAC African Sub 10404 C=1.00000 T=0.00000
ExAC Other Sub 908 C=1.000 T=0.000
Allele Frequency Aggregator Total Global 11862 C=1.00000 G=0.00000, T=0.00000
Allele Frequency Aggregator European Sub 7618 C=1.0000 G=0.0000, T=0.0000
Allele Frequency Aggregator African Sub 2816 C=1.0000 G=0.0000, T=0.0000
Allele Frequency Aggregator Latin American 2 Sub 610 C=1.000 G=0.000, T=0.000
Allele Frequency Aggregator Other Sub 470 C=1.000 G=0.000, T=0.000
Allele Frequency Aggregator Latin American 1 Sub 146 C=1.000 G=0.000, T=0.000
Allele Frequency Aggregator Asian Sub 108 C=1.000 G=0.000, T=0.000
Allele Frequency Aggregator South Asian Sub 94 C=1.00 G=0.00, T=0.00
1000Genomes_30x Global Study-wide 6404 C=0.9995 T=0.0005
1000Genomes_30x African Sub 1786 C=1.0000 T=0.0000
1000Genomes_30x Europe Sub 1266 C=1.0000 T=0.0000
1000Genomes_30x South Asian Sub 1202 C=0.9975 T=0.0025
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=0.9996 T=0.0004
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=1.0000 T=0.0000
1000Genomes South Asian Sub 978 C=0.998 T=0.002
1000Genomes American Sub 694 C=1.000 T=0.000
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 11 NC_000011.10:g.66026217C>G
GRCh38.p14 chr 11 NC_000011.10:g.66026217C>T
GRCh37.p13 chr 11 NC_000011.9:g.65793688C>G
GRCh37.p13 chr 11 NC_000011.9:g.65793688C>T
CATSPER1 RefSeqGene NG_016285.1:g.5301G>C
CATSPER1 RefSeqGene NG_016285.1:g.5301G>A
Gene: CATSPER1, cation channel sperm associated 1 (minus strand)
Molecule type Change Amino acid[Codon] SO Term
CATSPER1 transcript NM_053054.4:c.163G>C G [GGT] > R [CGT] Coding Sequence Variant
cation channel sperm-associated protein 1 NP_444282.3:p.Gly55Arg G (Gly) > R (Arg) Missense Variant
CATSPER1 transcript NM_053054.4:c.163G>A G [GGT] > S [AGT] Coding Sequence Variant
cation channel sperm-associated protein 1 NP_444282.3:p.Gly55Ser G (Gly) > S (Ser) Missense Variant
CATSPER1 transcript variant X1 XM_047426337.1:c.163G>C G [GGT] > R [CGT] Coding Sequence Variant
cation channel sperm-associated protein 1 isoform X1 XP_047282293.1:p.Gly55Arg G (Gly) > R (Arg) Missense Variant
CATSPER1 transcript variant X1 XM_047426337.1:c.163G>A G [GGT] > S [AGT] Coding Sequence Variant
cation channel sperm-associated protein 1 isoform X1 XP_047282293.1:p.Gly55Ser G (Gly) > S (Ser) Missense Variant
CATSPER1 transcript variant X3 XM_047426338.1:c.163G>C G [GGT] > R [CGT] Coding Sequence Variant
cation channel sperm-associated protein 1 isoform X2 XP_047282294.1:p.Gly55Arg G (Gly) > R (Arg) Missense Variant
CATSPER1 transcript variant X3 XM_047426338.1:c.163G>A G [GGT] > S [AGT] Coding Sequence Variant
cation channel sperm-associated protein 1 isoform X2 XP_047282294.1:p.Gly55Ser G (Gly) > S (Ser) Missense Variant
CATSPER1 transcript variant X2 XR_002957121.2:n.263G>C N/A Non Coding Transcript Variant
CATSPER1 transcript variant X2 XR_002957121.2:n.263G>A N/A Non Coding 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 T
GRCh38.p14 chr 11 NC_000011.10:g.66026217= NC_000011.10:g.66026217C>G NC_000011.10:g.66026217C>T
GRCh37.p13 chr 11 NC_000011.9:g.65793688= NC_000011.9:g.65793688C>G NC_000011.9:g.65793688C>T
CATSPER1 RefSeqGene NG_016285.1:g.5301= NG_016285.1:g.5301G>C NG_016285.1:g.5301G>A
CATSPER1 transcript NM_053054.4:c.163= NM_053054.4:c.163G>C NM_053054.4:c.163G>A
CATSPER1 transcript NM_053054.3:c.163= NM_053054.3:c.163G>C NM_053054.3:c.163G>A
CATSPER1 transcript variant X2 XR_002957121.2:n.263= XR_002957121.2:n.263G>C XR_002957121.2:n.263G>A
CATSPER1 transcript variant X2 XR_002957121.1:n.301= XR_002957121.1:n.301G>C XR_002957121.1:n.301G>A
CATSPER1 transcript variant X1 XM_047426337.1:c.163= XM_047426337.1:c.163G>C XM_047426337.1:c.163G>A
CATSPER1 transcript variant X3 XM_047426338.1:c.163= XM_047426338.1:c.163G>C XM_047426338.1:c.163G>A
cation channel sperm-associated protein 1 NP_444282.3:p.Gly55= NP_444282.3:p.Gly55Arg NP_444282.3:p.Gly55Ser
cation channel sperm-associated protein 1 isoform X1 XP_047282293.1:p.Gly55= XP_047282293.1:p.Gly55Arg XP_047282293.1:p.Gly55Ser
cation channel sperm-associated protein 1 isoform X2 XP_047282294.1:p.Gly55= XP_047282294.1:p.Gly55Arg XP_047282294.1:p.Gly55Ser
LOC101927968 transcript XM_005274422.1:c.-138+777= XM_005274422.1:c.-138+777C>G XM_005274422.1:c.-138+777C>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#.

9 SubSNP, 7 Frequency submissions
No Submitter Submission ID Date (Build)
1 1000GENOMES ss1341644126 Aug 21, 2014 (142)
2 EVA_EXAC ss1690480574 Apr 01, 2015 (144)
3 GNOMAD ss2739144892 Nov 08, 2017 (151)
4 GNOMAD ss4236695975 Apr 26, 2021 (155)
5 GNOMAD ss4236695976 Apr 26, 2021 (155)
6 1000G_HIGH_COVERAGE ss5287743959 Oct 16, 2022 (156)
7 EVA ss5400157539 Oct 16, 2022 (156)
8 1000G_HIGH_COVERAGE ss5583630631 Oct 16, 2022 (156)
9 EVA ss5920343558 Oct 16, 2022 (156)
10 1000Genomes NC_000011.9 - 65793688 Oct 12, 2018 (152)
11 1000Genomes_30x NC_000011.10 - 66026217 Oct 16, 2022 (156)
12 ExAC NC_000011.9 - 65793688 Oct 12, 2018 (152)
13 gnomAD - Genomes

Submission ignored due to conflicting rows:
Row 382443755 (NC_000011.10:66026216:C:G 1/140200)
Row 382443756 (NC_000011.10:66026216:C:T 0/140200)

- Apr 26, 2021 (155)
14 gnomAD - Genomes

Submission ignored due to conflicting rows:
Row 382443755 (NC_000011.10:66026216:C:G 1/140200)
Row 382443756 (NC_000011.10:66026216:C:T 0/140200)

- Apr 26, 2021 (155)
15 gnomAD - Exomes NC_000011.9 - 65793688 Jul 13, 2019 (153)
16 ALFA NC_000011.10 - 66026217 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
3636953900, ss4236695975 NC_000011.10:66026216:C:G NC_000011.10:66026216:C:G (self)
54179460, 744769, 8361058, ss1341644126, ss1690480574, ss2739144892, ss5400157539 NC_000011.9:65793687:C:T NC_000011.10:66026216:C:T (self)
71156566, 3636953900, ss4236695976, ss5287743959, ss5583630631, ss5920343558 NC_000011.10:66026216:C:T NC_000011.10:66026216: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 rs576598349

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