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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.

rs16870438

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr4:21136151 (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
T>C
Variation Type
SNV Single Nucleotide Variation
Frequency
C=0.019657 (5203/264690, TOPMED)
C=0.018337 (2571/140212, GnomAD)
C=0.01053 (199/18890, ALFA) (+ 6 more)
C=0.0242 (155/6404, 1000G_30x)
C=0.0228 (114/5008, 1000G)
C=0.0005 (2/3854, ALSPAC)
C=0.0003 (1/3708, TWINSUK)
C=0.019 (4/216, Qatari)
T=0.42 (10/24, SGDP_PRJ)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
KCNIP4 : 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 18890 T=0.98947 C=0.01053
European Sub 14286 T=0.99944 C=0.00056
African Sub 2946 T=0.9413 C=0.0587
African Others Sub 114 T=0.939 C=0.061
African American Sub 2832 T=0.9414 C=0.0586
Asian Sub 112 T=1.000 C=0.000
East Asian Sub 86 T=1.00 C=0.00
Other Asian Sub 26 T=1.00 C=0.00
Latin American 1 Sub 146 T=0.993 C=0.007
Latin American 2 Sub 610 T=0.993 C=0.007
South Asian Sub 98 T=1.00 C=0.00
Other Sub 692 T=0.981 C=0.019


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 T=0.980343 C=0.019657
gnomAD - Genomes Global Study-wide 140212 T=0.981663 C=0.018337
gnomAD - Genomes European Sub 75950 T=0.99971 C=0.00029
gnomAD - Genomes African Sub 42016 T=0.94288 C=0.05712
gnomAD - Genomes American Sub 13646 T=0.99106 C=0.00894
gnomAD - Genomes Ashkenazi Jewish Sub 3322 T=1.0000 C=0.0000
gnomAD - Genomes East Asian Sub 3128 T=1.0000 C=0.0000
gnomAD - Genomes Other Sub 2150 T=0.9874 C=0.0126
Allele Frequency Aggregator Total Global 18890 T=0.98947 C=0.01053
Allele Frequency Aggregator European Sub 14286 T=0.99944 C=0.00056
Allele Frequency Aggregator African Sub 2946 T=0.9413 C=0.0587
Allele Frequency Aggregator Other Sub 692 T=0.981 C=0.019
Allele Frequency Aggregator Latin American 2 Sub 610 T=0.993 C=0.007
Allele Frequency Aggregator Latin American 1 Sub 146 T=0.993 C=0.007
Allele Frequency Aggregator Asian Sub 112 T=1.000 C=0.000
Allele Frequency Aggregator South Asian Sub 98 T=1.00 C=0.00
1000Genomes_30x Global Study-wide 6404 T=0.9758 C=0.0242
1000Genomes_30x African Sub 1786 T=0.9188 C=0.0812
1000Genomes_30x Europe Sub 1266 T=1.0000 C=0.0000
1000Genomes_30x South Asian Sub 1202 T=1.0000 C=0.0000
1000Genomes_30x East Asian Sub 1170 T=1.0000 C=0.0000
1000Genomes_30x American Sub 980 T=0.990 C=0.010
1000Genomes Global Study-wide 5008 T=0.9772 C=0.0228
1000Genomes African Sub 1322 T=0.9183 C=0.0817
1000Genomes East Asian Sub 1008 T=1.0000 C=0.0000
1000Genomes Europe Sub 1006 T=1.0000 C=0.0000
1000Genomes South Asian Sub 978 T=1.000 C=0.000
1000Genomes American Sub 694 T=0.991 C=0.009
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 T=0.9995 C=0.0005
UK 10K study - Twins TWIN COHORT Study-wide 3708 T=0.9997 C=0.0003
Qatari Global Study-wide 216 T=0.981 C=0.019
SGDP_PRJ Global Study-wide 24 T=0.42 C=0.58
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 4 NC_000004.12:g.21136151T>C
GRCh37.p13 chr 4 NC_000004.11:g.21137774T>C
KCNIP4 RefSeqGene NG_052969.1:g.817601A>G
Gene: KCNIP4, potassium voltage-gated channel interacting protein 4 (minus strand)
Molecule type Change Amino acid[Codon] SO Term
KCNIP4 transcript variant 5 NM_001035003.2:c.89-28548…

NM_001035003.2:c.89-285484A>G

N/A Intron Variant
KCNIP4 transcript variant 6 NM_001035004.2:c.-23-2854…

NM_001035004.2:c.-23-285484A>G

N/A Intron Variant
KCNIP4 transcript variant 1 NM_025221.6:c.62-253442A>G N/A Intron Variant
KCNIP4 transcript variant 2 NM_147181.4:c.62-285484A>G N/A Intron Variant
KCNIP4 transcript variant 3 NM_147182.4:c.-23-285484A…

NM_147182.4:c.-23-285484A>G

N/A Intron Variant
KCNIP4 transcript variant 4 NM_147183.3:c.100+167656A…

NM_147183.3:c.100+167656A>G

N/A Intron Variant
KCNIP4 transcript variant 7 NM_001363504.2:c. N/A Genic Upstream Transcript Variant
KCNIP4 transcript variant X1 XM_011513885.4:c.89-28548…

XM_011513885.4:c.89-285484A>G

N/A Intron 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 T= C
GRCh38.p14 chr 4 NC_000004.12:g.21136151= NC_000004.12:g.21136151T>C
GRCh37.p13 chr 4 NC_000004.11:g.21137774= NC_000004.11:g.21137774T>C
KCNIP4 RefSeqGene NG_052969.1:g.817601= NG_052969.1:g.817601A>G
KCNIP4 transcript variant 5 NM_001035003.1:c.89-285484= NM_001035003.1:c.89-285484A>G
KCNIP4 transcript variant 5 NM_001035003.2:c.89-285484= NM_001035003.2:c.89-285484A>G
KCNIP4 transcript variant 6 NM_001035004.1:c.-23-285484= NM_001035004.1:c.-23-285484A>G
KCNIP4 transcript variant 6 NM_001035004.2:c.-23-285484= NM_001035004.2:c.-23-285484A>G
KCNIP4 transcript variant 1 NM_025221.5:c.62-253442= NM_025221.5:c.62-253442A>G
KCNIP4 transcript variant 1 NM_025221.6:c.62-253442= NM_025221.6:c.62-253442A>G
KCNIP4 transcript variant 2 NM_147181.3:c.62-285484= NM_147181.3:c.62-285484A>G
KCNIP4 transcript variant 2 NM_147181.4:c.62-285484= NM_147181.4:c.62-285484A>G
KCNIP4 transcript variant 3 NM_147182.3:c.-23-285484= NM_147182.3:c.-23-285484A>G
KCNIP4 transcript variant 3 NM_147182.4:c.-23-285484= NM_147182.4:c.-23-285484A>G
KCNIP4 transcript variant 4 NM_147183.3:c.100+167656= NM_147183.3:c.100+167656A>G
KCNIP4 transcript variant X2 XM_005248189.1:c.100+167656= XM_005248189.1:c.100+167656A>G
KCNIP4 transcript variant X4 XM_005248191.1:c.62-285484= XM_005248191.1:c.62-285484A>G
KCNIP4 transcript variant X1 XM_011513885.4:c.89-285484= XM_011513885.4:c.89-285484A>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#.

24 SubSNP, 9 Frequency submissions
No Submitter Submission ID Date (Build)
1 PERLEGEN ss23315608 Sep 20, 2004 (123)
2 1000GENOMES ss220786651 Jul 14, 2010 (132)
3 TISHKOFF ss557362512 Apr 25, 2013 (138)
4 JMKIDD_LAB ss1071338238 Aug 21, 2014 (142)
5 1000GENOMES ss1308752095 Aug 21, 2014 (142)
6 EVA_DECODE ss1589342241 Apr 01, 2015 (144)
7 EVA_UK10K_ALSPAC ss1609579771 Apr 01, 2015 (144)
8 EVA_UK10K_TWINSUK ss1652573804 Apr 01, 2015 (144)
9 HAMMER_LAB ss1801106762 Sep 08, 2015 (146)
10 WEILL_CORNELL_DGM ss1923088007 Feb 12, 2016 (147)
11 HUMAN_LONGEVITY ss2261059329 Dec 20, 2016 (150)
12 GNOMAD ss2806527165 Nov 08, 2017 (151)
13 EVA_DECODE ss3711566798 Jul 13, 2019 (153)
14 KHV_HUMAN_GENOMES ss3804630558 Jul 13, 2019 (153)
15 SGDP_PRJ ss3858392203 Apr 26, 2020 (154)
16 TOPMED ss4605557162 Apr 26, 2021 (155)
17 1000G_HIGH_COVERAGE ss5258325300 Oct 13, 2022 (156)
18 EVA ss5347416311 Oct 13, 2022 (156)
19 HUGCELL_USP ss5457195674 Oct 13, 2022 (156)
20 EVA ss5507416968 Oct 13, 2022 (156)
21 1000G_HIGH_COVERAGE ss5538906930 Oct 13, 2022 (156)
22 SANFORD_IMAGENETICS ss5634511646 Oct 13, 2022 (156)
23 EVA ss5862466562 Oct 13, 2022 (156)
24 EVA ss5962894277 Oct 13, 2022 (156)
25 1000Genomes NC_000004.11 - 21137774 Oct 12, 2018 (152)
26 1000Genomes_30x NC_000004.12 - 21136151 Oct 13, 2022 (156)
27 The Avon Longitudinal Study of Parents and Children NC_000004.11 - 21137774 Oct 12, 2018 (152)
28 gnomAD - Genomes NC_000004.12 - 21136151 Apr 26, 2021 (155)
29 Qatari NC_000004.11 - 21137774 Apr 26, 2020 (154)
30 SGDP_PRJ NC_000004.11 - 21137774 Apr 26, 2020 (154)
31 TopMed NC_000004.12 - 21136151 Apr 26, 2021 (155)
32 UK 10K study - Twins NC_000004.11 - 21137774 Oct 12, 2018 (152)
33 ALFA NC_000004.12 - 21136151 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
ss1589342241 NC_000004.10:20746871:T:C NC_000004.12:21136150:T:C (self)
20110877, 11202915, 5129937, 10409183, 11202915, ss220786651, ss557362512, ss1071338238, ss1308752095, ss1609579771, ss1652573804, ss1801106762, ss1923088007, ss2806527165, ss3858392203, ss5347416311, ss5507416968, ss5634511646, ss5962894277 NC_000004.11:21137773:T:C NC_000004.12:21136150:T:C (self)
26432865, 142520461, 442934718, 11195289046, ss2261059329, ss3711566798, ss3804630558, ss4605557162, ss5258325300, ss5457195674, ss5538906930, ss5862466562 NC_000004.12:21136150:T:C NC_000004.12:21136150:T:C (self)
ss23315608 NT_006316.16:12319570:T:C NC_000004.12:21136150:T: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 rs16870438

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