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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.

rs141725436

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr19:33798683 (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=0.005924 (1568/264690, TOPMED)
A=0.006058 (850/140310, GnomAD)
A=0.00730 (140/19190, ALFA) (+ 12 more)
A=0.0025 (16/6404, 1000G_30x)
A=0.0026 (13/5008, 1000G)
A=0.0065 (29/4480, Estonian)
A=0.0067 (26/3854, ALSPAC)
A=0.0073 (27/3708, TWINSUK)
A=0.011 (11/998, GoNL)
A=0.022 (13/600, NorthernSweden)
A=0.011 (6/534, MGP)
A=0.005 (1/216, Qatari)
A=0.03 (1/40, GENOME_DK)
G=0.5 (1/2, SGDP_PRJ)
A=0.5 (1/2, SGDP_PRJ)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
KCTD15 : 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 19190 G=0.99270 A=0.00730
European Sub 14286 G=0.99132 A=0.00868
African Sub 2970 G=0.9983 A=0.0017
African Others Sub 114 G=1.000 A=0.000
African American Sub 2856 G=0.9982 A=0.0018
Asian Sub 116 G=1.000 A=0.000
East Asian Sub 88 G=1.00 A=0.00
Other Asian Sub 28 G=1.00 A=0.00
Latin American 1 Sub 154 G=0.994 A=0.006
Latin American 2 Sub 616 G=0.995 A=0.005
South Asian Sub 98 G=1.00 A=0.00
Other Sub 950 G=0.993 A=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=0.994076 A=0.005924
gnomAD - Genomes Global Study-wide 140310 G=0.993942 A=0.006058
gnomAD - Genomes European Sub 75966 G=0.99148 A=0.00852
gnomAD - Genomes African Sub 42066 G=0.99826 A=0.00174
gnomAD - Genomes American Sub 13666 G=0.99415 A=0.00585
gnomAD - Genomes Ashkenazi Jewish Sub 3324 G=0.9901 A=0.0099
gnomAD - Genomes East Asian Sub 3134 G=1.0000 A=0.0000
gnomAD - Genomes Other Sub 2154 G=0.9921 A=0.0079
Allele Frequency Aggregator Total Global 19190 G=0.99270 A=0.00730
Allele Frequency Aggregator European Sub 14286 G=0.99132 A=0.00868
Allele Frequency Aggregator African Sub 2970 G=0.9983 A=0.0017
Allele Frequency Aggregator Other Sub 950 G=0.993 A=0.007
Allele Frequency Aggregator Latin American 2 Sub 616 G=0.995 A=0.005
Allele Frequency Aggregator Latin American 1 Sub 154 G=0.994 A=0.006
Allele Frequency Aggregator Asian Sub 116 G=1.000 A=0.000
Allele Frequency Aggregator South Asian Sub 98 G=1.00 A=0.00
1000Genomes_30x Global Study-wide 6404 G=0.9975 A=0.0025
1000Genomes_30x African Sub 1786 G=1.0000 A=0.0000
1000Genomes_30x Europe Sub 1266 G=0.9921 A=0.0079
1000Genomes_30x South Asian Sub 1202 G=1.0000 A=0.0000
1000Genomes_30x East Asian Sub 1170 G=1.0000 A=0.0000
1000Genomes_30x American Sub 980 G=0.994 A=0.006
1000Genomes Global Study-wide 5008 G=0.9974 A=0.0026
1000Genomes African Sub 1322 G=1.0000 A=0.0000
1000Genomes East Asian Sub 1008 G=1.0000 A=0.0000
1000Genomes Europe Sub 1006 G=0.9911 A=0.0089
1000Genomes South Asian Sub 978 G=1.000 A=0.000
1000Genomes American Sub 694 G=0.994 A=0.006
Genetic variation in the Estonian population Estonian Study-wide 4480 G=0.9935 A=0.0065
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 G=0.9933 A=0.0067
UK 10K study - Twins TWIN COHORT Study-wide 3708 G=0.9927 A=0.0073
Genome of the Netherlands Release 5 Genome of the Netherlands Study-wide 998 G=0.989 A=0.011
Northern Sweden ACPOP Study-wide 600 G=0.978 A=0.022
Medical Genome Project healthy controls from Spanish population Spanish controls Study-wide 534 G=0.989 A=0.011
Qatari Global Study-wide 216 G=0.995 A=0.005
The Danish reference pan genome Danish Study-wide 40 G=0.97 A=0.03
SGDP_PRJ Global Study-wide 2 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 19 NC_000019.10:g.33798683G>A
GRCh37.p13 chr 19 NC_000019.9:g.34289588G>A
Gene: KCTD15, potassium channel tetramerization domain containing 15 (plus strand)
Molecule type Change Amino acid[Codon] SO Term
KCTD15 transcript variant 2 NM_001129994.2:c.-111= N/A 5 Prime UTR Variant
KCTD15 transcript variant 3 NM_001129995.2:c.-111= N/A 5 Prime UTR Variant
KCTD15 transcript variant 1 NM_024076.3:c.-111= N/A 5 Prime UTR Variant
KCTD15 transcript variant X2 XM_047439393.1:c.-111= N/A 5 Prime UTR Variant
KCTD15 transcript variant X3 XM_047439394.1:c.-111= N/A 5 Prime UTR Variant
KCTD15 transcript variant X4 XM_047439395.1:c.-111= N/A 5 Prime UTR Variant
KCTD15 transcript variant X5 XM_047439396.1:c.-111= N/A 5 Prime UTR Variant
KCTD15 transcript variant X6 XM_047439397.1:c.-111= N/A 5 Prime UTR Variant
KCTD15 transcript variant X7 XM_047439398.1:c.-111= N/A 5 Prime UTR Variant
KCTD15 transcript variant X8 XM_011527296.3:c.-236= N/A 5 Prime UTR Variant
KCTD15 transcript variant X9 XM_011527298.3:c.-236= N/A 5 Prime UTR Variant
KCTD15 transcript variant X10 XM_017027283.2:c.-236= N/A 5 Prime UTR Variant
KCTD15 transcript variant X11 XM_011527297.3:c.-236= N/A 5 Prime UTR Variant
KCTD15 transcript variant X12 XM_047439399.1:c.-111= N/A 5 Prime UTR Variant
KCTD15 transcript variant X13 XM_047439400.1:c.-111= N/A 5 Prime UTR Variant
KCTD15 transcript variant X14 XM_047439401.1:c.-111= N/A 5 Prime UTR Variant
KCTD15 transcript variant X15 XM_047439402.1:c.-111= N/A 5 Prime UTR Variant
KCTD15 transcript variant X1 XM_047439392.1:c. N/A Genic Upstream Transcript Variant
KCTD15 transcript variant X16 XM_017027284.2:c.485G>A R [AGA] > K [AAA] Coding Sequence Variant
BTB/POZ domain-containing protein KCTD15 isoform X4 XP_016882773.1:p.Arg162Lys R (Arg) > K (Lys) Missense 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 19 NC_000019.10:g.33798683= NC_000019.10:g.33798683G>A
GRCh37.p13 chr 19 NC_000019.9:g.34289588= NC_000019.9:g.34289588G>A
KCTD15 transcript variant 1 NM_024076.3:c.-111= NM_024076.3:c.-111G>A
KCTD15 transcript variant 1 NM_024076.2:c.-111= NM_024076.2:c.-111G>A
KCTD15 transcript variant X8 XM_011527296.3:c.-236= XM_011527296.3:c.-236G>A
KCTD15 transcript variant X1 XM_011527296.2:c.-236= XM_011527296.2:c.-236G>A
KCTD15 transcript variant X1 XM_011527296.1:c.-612= XM_011527296.1:c.-612G>A
KCTD15 transcript variant X11 XM_011527297.3:c.-236= XM_011527297.3:c.-236G>A
KCTD15 transcript variant X2 XM_011527297.2:c.-236= XM_011527297.2:c.-236G>A
KCTD15 transcript variant X2 XM_011527297.1:c.-236= XM_011527297.1:c.-236G>A
KCTD15 transcript variant X9 XM_011527298.3:c.-236= XM_011527298.3:c.-236G>A
KCTD15 transcript variant X3 XM_011527298.2:c.-236= XM_011527298.2:c.-236G>A
KCTD15 transcript variant X3 XM_011527298.1:c.-236= XM_011527298.1:c.-236G>A
KCTD15 transcript variant X10 XM_017027283.2:c.-236= XM_017027283.2:c.-236G>A
KCTD15 transcript variant X4 XM_017027283.1:c.-236= XM_017027283.1:c.-236G>A
KCTD15 transcript variant 2 NM_001129994.2:c.-111= NM_001129994.2:c.-111G>A
KCTD15 transcript variant 2 NM_001129994.1:c.-111= NM_001129994.1:c.-111G>A
KCTD15 transcript variant 3 NM_001129995.2:c.-111= NM_001129995.2:c.-111G>A
KCTD15 transcript variant 3 NM_001129995.1:c.-111= NM_001129995.1:c.-111G>A
KCTD15 transcript variant X16 XM_017027284.2:c.485= XM_017027284.2:c.485G>A
KCTD15 transcript variant X6 XM_017027284.1:c.485= XM_017027284.1:c.485G>A
KCTD15 transcript variant X6 XM_047439397.1:c.-111= XM_047439397.1:c.-111G>A
KCTD15 transcript variant X2 XM_047439393.1:c.-111= XM_047439393.1:c.-111G>A
KCTD15 transcript variant X12 XM_047439399.1:c.-111= XM_047439399.1:c.-111G>A
KCTD15 transcript variant X4 XM_047439395.1:c.-111= XM_047439395.1:c.-111G>A
KCTD15 transcript variant X7 XM_047439398.1:c.-111= XM_047439398.1:c.-111G>A
KCTD15 transcript variant X3 XM_047439394.1:c.-111= XM_047439394.1:c.-111G>A
KCTD15 transcript variant X5 XM_047439396.1:c.-111= XM_047439396.1:c.-111G>A
KCTD15 transcript variant X13 XM_047439400.1:c.-111= XM_047439400.1:c.-111G>A
KCTD15 transcript variant X14 XM_047439401.1:c.-111= XM_047439401.1:c.-111G>A
KCTD15 transcript variant X15 XM_047439402.1:c.-111= XM_047439402.1:c.-111G>A
BTB/POZ domain-containing protein KCTD15 isoform X4 XP_016882773.1:p.Arg162= XP_016882773.1:p.Arg162Lys
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#.

32 SubSNP, 14 Frequency submissions
No Submitter Submission ID Date (Build)
1 1000GENOMES ss340433460 May 09, 2011 (134)
2 ILLUMINA ss535225753 Sep 08, 2015 (146)
3 EVA-GONL ss994256774 Aug 21, 2014 (142)
4 JMKIDD_LAB ss1081874914 Aug 21, 2014 (142)
5 1000GENOMES ss1362998700 Aug 21, 2014 (142)
6 EVA_GENOME_DK ss1578623708 Apr 01, 2015 (144)
7 EVA_UK10K_ALSPAC ss1637885558 Apr 01, 2015 (144)
8 EVA_UK10K_TWINSUK ss1680879591 Apr 01, 2015 (144)
9 EVA_DECODE ss1698309829 Apr 01, 2015 (144)
10 EVA_MGP ss1711509192 Apr 01, 2015 (144)
11 WEILL_CORNELL_DGM ss1937750360 Feb 12, 2016 (147)
12 JJLAB ss2029652337 Sep 14, 2016 (149)
13 HUMAN_LONGEVITY ss2225435351 Dec 20, 2016 (150)
14 GNOMAD ss2962369542 Nov 08, 2017 (151)
15 AFFY ss2985138955 Nov 08, 2017 (151)
16 SWEGEN ss3017397203 Nov 08, 2017 (151)
17 ILLUMINA ss3627922182 Oct 12, 2018 (152)
18 EGCUT_WGS ss3684174375 Jul 13, 2019 (153)
19 EVA_DECODE ss3702681641 Jul 13, 2019 (153)
20 ACPOP ss3743001045 Jul 13, 2019 (153)
21 EVA ss3756013446 Jul 13, 2019 (153)
22 EVA ss3825932901 Apr 27, 2020 (154)
23 SGDP_PRJ ss3888126427 Apr 27, 2020 (154)
24 TOPMED ss5073390082 Apr 26, 2021 (155)
25 1000G_HIGH_COVERAGE ss5307093402 Oct 16, 2022 (156)
26 EVA ss5434575822 Oct 16, 2022 (156)
27 HUGCELL_USP ss5499638732 Oct 16, 2022 (156)
28 1000G_HIGH_COVERAGE ss5612756256 Oct 16, 2022 (156)
29 SANFORD_IMAGENETICS ss5662307548 Oct 16, 2022 (156)
30 EVA ss5840490963 Oct 16, 2022 (156)
31 EVA ss5927938821 Oct 16, 2022 (156)
32 EVA ss5953723233 Oct 16, 2022 (156)
33 1000Genomes NC_000019.9 - 34289588 Oct 12, 2018 (152)
34 1000Genomes_30x NC_000019.10 - 33798683 Oct 16, 2022 (156)
35 The Avon Longitudinal Study of Parents and Children NC_000019.9 - 34289588 Oct 12, 2018 (152)
36 Genetic variation in the Estonian population NC_000019.9 - 34289588 Oct 12, 2018 (152)
37 The Danish reference pan genome NC_000019.9 - 34289588 Apr 27, 2020 (154)
38 gnomAD - Genomes NC_000019.10 - 33798683 Apr 26, 2021 (155)
39 Genome of the Netherlands Release 5 NC_000019.9 - 34289588 Apr 27, 2020 (154)
40 Medical Genome Project healthy controls from Spanish population NC_000019.9 - 34289588 Apr 27, 2020 (154)
41 Northern Sweden NC_000019.9 - 34289588 Jul 13, 2019 (153)
42 Qatari NC_000019.9 - 34289588 Apr 27, 2020 (154)
43 SGDP_PRJ NC_000019.9 - 34289588 Apr 27, 2020 (154)
44 TopMed NC_000019.10 - 33798683 Apr 26, 2021 (155)
45 UK 10K study - Twins NC_000019.9 - 34289588 Oct 12, 2018 (152)
46 ALFA NC_000019.10 - 33798683 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)
rs386474429 Aug 21, 2014 (142)
Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
ss1698309829 NC_000019.8:38981427:G:A NC_000019.10:33798682:G:A (self)
76399573, 42317524, 29912623, 4806867, 18853025, 624952, 16285910, 19792282, 40143407, 42317524, ss340433460, ss535225753, ss994256774, ss1081874914, ss1362998700, ss1578623708, ss1637885558, ss1680879591, ss1711509192, ss1937750360, ss2029652337, ss2962369542, ss2985138955, ss3017397203, ss3627922182, ss3684174375, ss3743001045, ss3756013446, ss3825932901, ss3888126427, ss5434575822, ss5662307548, ss5840490963, ss5953723233 NC_000019.9:34289587:G:A NC_000019.10:33798682:G:A (self)
100282191, 538806160, 288935746, 13968316514, ss2225435351, ss3702681641, ss5073390082, ss5307093402, ss5499638732, ss5612756256, ss5927938821 NC_000019.10:33798682:G:A NC_000019.10:33798682: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 rs141725436

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