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dbSNP Short Genetic Variations

Reference SNP (rs) Report

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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.

rs1572591

Current Build 151

Released July 17, 2018

Organism
Homo sapiens
Position
chr13:101407725 (GRCh38.p7) 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
C=0.33750 (42379/125568, TOPMED)
C=0.3629 (11216/30910, GnomAD)
C=0.275 (1375/5008, 1000G) (+ 2 more)
C=0.494 (1902/3854, ALSPAC)
C=0.496 (1838/3708, TWINSUK)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
NALCN : Intron 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.p7 chr 13 NC_000013.11:g.101407725C>G
GRCh38.p7 chr 13 NC_000013.11:g.101407725C>T
GRCh37.p13 chr 13 NC_000013.10:g.102060076C>G
GRCh37.p13 chr 13 NC_000013.10:g.102060076C>T
Gene: NALCN, sodium leak channel, non-selective (minus strand)
Molecule type Change Amino acid[Codon] SO Term
NALCN transcript NM_052867.2:c. N/A Intron Variant
NALCN transcript variant X1 XM_011521067.2:c. N/A Intron Variant
NALCN transcript variant X2 XM_011521068.2:c. N/A Intron Variant
NALCN transcript variant X2 XM_011521069.2:c. N/A Intron Variant
NALCN transcript variant X4 XM_017020534.1:c. N/A Intron Variant
NALCN transcript variant X5 XM_017020535.1:c. N/A Intron Variant
NALCN transcript variant X6 XM_017020536.1:c. N/A Genic Upstream Transcript Variant
NALCN transcript variant X4 XM_017020537.1:c. N/A Genic 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
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").

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Study Population Group Sample Size Ref Allele Alt Allele
Trans-Omics for Precision Medicine Global Study-wide 125568 C=0.33750 T=0.66250
The Genome Aggregation Database Global Study-wide 30910 C=0.3629 T=0.6371
The Genome Aggregation Database European Sub 18450 C=0.4842 T=0.5158
The Genome Aggregation Database African Sub 8730 C=0.134 T=0.866
The Genome Aggregation Database East Asian Sub 1612 C=0.186 T=0.814
The Genome Aggregation Database Other Sub 980 C=0.43 T=0.57
The Genome Aggregation Database American Sub 836 C=0.29 T=0.71
The Genome Aggregation Database Ashkenazi Jewish Sub 302 C=0.49 T=0.51
1000Genomes Global Study-wide 5008 C=0.275 T=0.725
1000Genomes African Sub 1322 C=0.088 T=0.912
1000Genomes East Asian Sub 1008 C=0.173 T=0.827
1000Genomes Europe Sub 1006 C=0.491 T=0.509
1000Genomes South Asian Sub 978 C=0.40 T=0.60
1000Genomes American Sub 694 C=0.29 T=0.71
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 C=0.494 T=0.506
UK 10K study - Twins TWIN COHORT Study-wide 3708 C=0.496 T=0.504
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 Note
GRCh38.p7 chr 13 NC_000013.11:g.10...

NC_000013.11:g.101407725C=

NC_000013.11:g.10...

NC_000013.11:g.101407725C>G

NC_000013.11:g.10...

NC_000013.11:g.101407725C>T

GRCh37.p13 chr 13 NC_000013.10:g.10...

NC_000013.10:g.102060076C=

NC_000013.10:g.10...

NC_000013.10:g.102060076C>G

NC_000013.10:g.10...

NC_000013.10:g.102060076C>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#.

5 Frequency, 67 SubSNP submissions
No Submitter Submission ID Date (Build)
1 TSC-CSHL ss2417280 Oct 23, 2000 (88)
2 SC_SNP ss13183065 Dec 05, 2003 (119)
3 CSHL-HAPMAP ss19282538 Feb 27, 2004 (120)
4 CSHL-HAPMAP ss19975177 Feb 27, 2004 (120)
5 SSAHASNP ss21080284 Apr 05, 2004 (121)
6 PERLEGEN ss69145367 May 17, 2007 (127)
7 AFFY ss76791799 Dec 06, 2007 (129)
8 HGSV ss77463441 Dec 06, 2007 (129)
9 HGSV ss78946773 Dec 06, 2007 (129)
10 HGSV ss82841670 Dec 15, 2007 (130)
11 HGSV ss85465261 Dec 15, 2007 (130)
12 BCMHGSC_JDW ss89823207 Mar 24, 2008 (129)
13 BGI ss103154733 Dec 01, 2009 (131)
14 KRIBB_YJKIM ss104850233 Feb 06, 2009 (130)
15 1000GENOMES ss108049691 Jan 22, 2009 (130)
16 1000GENOMES ss115204621 Jan 25, 2009 (130)
17 ILLUMINA-UK ss118969113 Feb 15, 2009 (130)
18 ENSEMBL ss132179786 Dec 01, 2009 (131)
19 ENSEMBL ss133795203 Dec 01, 2009 (131)
20 GMI ss155314388 Dec 01, 2009 (131)
21 COMPLETE_GENOMICS ss170615475 Jul 04, 2010 (132)
22 COMPLETE_GENOMICS ss171654349 Jul 04, 2010 (132)
23 BUSHMAN ss199636083 Jul 04, 2010 (132)
24 BCM-HGSC-SUB ss208688129 Jul 04, 2010 (132)
25 1000GENOMES ss226381545 Jul 14, 2010 (132)
26 1000GENOMES ss236403875 Jul 15, 2010 (132)
27 1000GENOMES ss242865691 Jul 15, 2010 (132)
28 GMI ss281859525 May 04, 2012 (137)
29 GMI ss286775888 Apr 25, 2013 (138)
30 PJP ss291521625 May 09, 2011 (134)
31 ILLUMINA ss481384496 May 04, 2012 (137)
32 ILLUMINA ss483140168 May 04, 2012 (137)
33 ILLUMINA ss534257155 Sep 08, 2015 (146)
34 TISHKOFF ss563881409 Apr 25, 2013 (138)
35 SSMP ss659525352 Apr 25, 2013 (138)
36 ILLUMINA ss779863683 Sep 08, 2015 (146)
37 ILLUMINA ss781468019 Sep 08, 2015 (146)
38 ILLUMINA ss835340852 Sep 08, 2015 (146)
39 EVA-GONL ss990783113 Aug 21, 2014 (142)
40 JMKIDD_LAB ss1079383547 Aug 21, 2014 (142)
41 1000GENOMES ss1349652891 Aug 21, 2014 (142)
42 DDI ss1427307309 Apr 01, 2015 (144)
43 EVA_GENOME_DK ss1577028342 Apr 01, 2015 (144)
44 EVA_UK10K_ALSPAC ss1631036462 Apr 01, 2015 (144)
45 EVA_UK10K_TWINSUK ss1674030495 Apr 01, 2015 (144)
46 EVA_DECODE ss1694774913 Apr 01, 2015 (144)
47 EVA_SVP ss1713418059 Apr 01, 2015 (144)
48 HAMMER_LAB ss1807765999 Sep 08, 2015 (146)
49 WEILL_CORNELL_DGM ss1934144740 Feb 12, 2016 (147)
50 GENOMED ss1967878497 Jul 19, 2016 (147)
51 JJLAB ss2027845710 Sep 14, 2016 (149)
52 USC_VALOUEV ss2156213232 Dec 20, 2016 (150)
53 HUMAN_LONGEVITY ss2199275107 Dec 20, 2016 (150)
54 TOPMED ss2363524122 Dec 20, 2016 (150)
55 SYSTEMSBIOZJU ss2628411035 Nov 08, 2017 (151)
56 ILLUMINA ss2633106454 Nov 08, 2017 (151)
57 GRF ss2700609719 Nov 08, 2017 (151)
58 GNOMAD ss2923746869 Nov 08, 2017 (151)
59 AFFY ss2985646234 Nov 08, 2017 (151)
60 SWEGEN ss3011611537 Nov 08, 2017 (151)
61 BIOINF_KMB_FNS_UNIBA ss3027744704 Nov 08, 2017 (151)
62 TOPMED ss3202180056 Nov 08, 2017 (151)
63 TOPMED ss3202180057 Nov 08, 2017 (151)
64 CSHL ss3350632140 Nov 08, 2017 (151)
65 ILLUMINA ss3627140488 Jul 20, 2018 (151)
66 ILLUMINA ss3631107435 Jul 20, 2018 (151)
67 ILLUMINA ss3641857609 Jul 20, 2018 (151)
68 1000Genomes NC_000013.10 - 102060076 Jul 20, 2018 (151)
69 The Avon Longitudinal Study of Parents and Children NC_000013.10 - 102060076 Jul 20, 2018 (151)
70 The Genome Aggregation Database NC_000013.10 - 102060076 Jul 20, 2018 (151)
71 Trans-Omics for Precision Medicine NC_000013.11 - 101407725 Jul 20, 2018 (151)
72 UK 10K study - Twins NC_000013.10 - 102060076 Jul 20, 2018 (151)
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)
rs60682557 May 26, 2008 (130)
Added to this RefSNP Cluster:
Submission ids Observation SPDI Canonical SPDI Source RSIDs
ss77463441, ss78946773, ss82841670, ss85465261, ss89823207, ss108049691, ss115204621, ss118969113, ss170615475, ss171654349, ss199636083, ss208688129, ss281859525, ss286775888, ss291521625, ss483140168, ss1694774913, ss1713418059 NC_000013.9:100858076:C= NC_000013.11:101407724:C= (self)
62581943, 34774200, 57448393, 34774200, ss226381545, ss236403875, ss242865691, ss481384496, ss534257155, ss563881409, ss659525352, ss779863683, ss781468019, ss835340852, ss990783113, ss1079383547, ss1349652891, ss1427307309, ss1577028342, ss1631036462, ss1674030495, ss1807765999, ss1934144740, ss1967878497, ss2027845710, ss2156213232, ss2363524122, ss2628411035, ss2633106454, ss2700609719, ss2923746869, ss2985646234, ss3011611537, ss3350632140, ss3627140488, ss3631107435, ss3641857609 NC_000013.10:102060075:C= NC_000013.11:101407724:C= (self)
109365196, ss2199275107, ss3027744704, ss3202180056, ss3202180057 NC_000013.11:101407724:C= NC_000013.11:101407724:C= (self)
ss13183065 NT_009952.13:15149751:C= NC_000013.11:101407724:C= (self)
ss2417280, ss19282538, ss19975177, ss21080284, ss69145367, ss76791799, ss103154733, ss104850233, ss132179786, ss133795203, ss155314388 NT_009952.14:15149751:C= NC_000013.11:101407724:C= (self)
ss3202180056 NC_000013.11:101407724:C>G NC_000013.11:101407724:C>G (self)
ss77463441, ss78946773, ss82841670, ss85465261, ss89823207, ss108049691, ss115204621, ss118969113, ss170615475, ss171654349, ss199636083, ss208688129, ss281859525, ss286775888, ss291521625, ss483140168, ss1694774913, ss1713418059 NC_000013.9:100858076:C>T NC_000013.11:101407724:C>T (self)
62581943, 34774200, 57448393, 34774200, ss226381545, ss236403875, ss242865691, ss481384496, ss534257155, ss563881409, ss659525352, ss779863683, ss781468019, ss835340852, ss990783113, ss1079383547, ss1349652891, ss1427307309, ss1577028342, ss1631036462, ss1674030495, ss1807765999, ss1934144740, ss1967878497, ss2027845710, ss2156213232, ss2363524122, ss2628411035, ss2633106454, ss2700609719, ss2923746869, ss2985646234, ss3011611537, ss3350632140, ss3627140488, ss3631107435, ss3641857609 NC_000013.10:102060075:C>T NC_000013.11:101407724:C>T (self)
109365196, ss2199275107, ss3027744704, ss3202180057 NC_000013.11:101407724:C>T NC_000013.11:101407724:C>T (self)
ss13183065 NT_009952.13:15149751:C>T NC_000013.11:101407724:C>T (self)
ss2417280, ss19282538, ss19975177, ss21080284, ss69145367, ss76791799, ss103154733, ss104850233, ss132179786, ss133795203, ss155314388 NT_009952.14:15149751:C>T NC_000013.11:101407724: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 rs1572591

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: 0.1.4.post833+d3ba21e