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dbSNP Short Genetic Variations

Examples: rs268, BRCA1 and more Advanced search

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.

rs200324727

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr15:58541923 (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>T
Variation Type
SNV Single Nucleotide Variation
Frequency
T=0.000034 (9/264690, TOPMED)
T=0.000101 (25/247790, GnomAD_exome)
T=0.000040 (7/172950, ALFA) (+ 7 more)
T=0.000071 (10/140286, GnomAD)
T=0.000118 (13/109924, ExAC)
T=0.00003 (2/78612, PAGE_STUDY)
T=0.00032 (9/28258, 14KJPN)
T=0.00030 (5/16760, 8.3KJPN)
T=0.0002 (1/4480, Estonian)
T=0.004 (1/282, FINRISK)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
LIPC : 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 173072 C=0.999960 T=0.000040
European Sub 151366 C=0.999980 T=0.000020
African Sub 4306 C=1.0000 T=0.0000
African Others Sub 168 C=1.000 T=0.000
African American Sub 4138 C=1.0000 T=0.0000
Asian Sub 6288 C=0.9997 T=0.0003
East Asian Sub 4472 C=1.0000 T=0.0000
Other Asian Sub 1816 C=0.9989 T=0.0011
Latin American 1 Sub 442 C=1.000 T=0.000
Latin American 2 Sub 950 C=1.000 T=0.000
South Asian Sub 280 C=1.000 T=0.000
Other Sub 9440 C=0.9998 T=0.0002


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=0.999966 T=0.000034
gnomAD - Exomes Global Study-wide 247790 C=0.999899 T=0.000101
gnomAD - Exomes European Sub 132530 C=0.999849 T=0.000151
gnomAD - Exomes Asian Sub 48648 C=0.99998 T=0.00002
gnomAD - Exomes American Sub 34454 C=0.99991 T=0.00009
gnomAD - Exomes African Sub 16040 C=0.99994 T=0.00006
gnomAD - Exomes Ashkenazi Jewish Sub 10042 C=1.00000 T=0.00000
gnomAD - Exomes Other Sub 6076 C=1.0000 T=0.0000
Allele Frequency Aggregator Total Global 172950 C=0.999960 T=0.000040
Allele Frequency Aggregator European Sub 151262 C=0.999980 T=0.000020
Allele Frequency Aggregator Other Sub 9436 C=0.9998 T=0.0002
Allele Frequency Aggregator Asian Sub 6288 C=0.9997 T=0.0003
Allele Frequency Aggregator African Sub 4292 C=1.0000 T=0.0000
Allele Frequency Aggregator Latin American 2 Sub 950 C=1.000 T=0.000
Allele Frequency Aggregator Latin American 1 Sub 442 C=1.000 T=0.000
Allele Frequency Aggregator South Asian Sub 280 C=1.000 T=0.000
gnomAD - Genomes Global Study-wide 140286 C=0.999929 T=0.000071
gnomAD - Genomes European Sub 75962 C=0.99991 T=0.00009
gnomAD - Genomes African Sub 42050 C=0.99995 T=0.00005
gnomAD - Genomes American Sub 13666 C=0.99993 T=0.00007
gnomAD - Genomes Ashkenazi Jewish Sub 3322 C=1.0000 T=0.0000
gnomAD - Genomes East Asian Sub 3134 C=1.0000 T=0.0000
gnomAD - Genomes Other Sub 2152 C=1.0000 T=0.0000
ExAC Global Study-wide 109924 C=0.999882 T=0.000118
ExAC Europe Sub 66380 C=0.99985 T=0.00015
ExAC Asian Sub 22756 C=0.99996 T=0.00004
ExAC American Sub 10816 C=0.99991 T=0.00009
ExAC African Sub 9170 C=0.9999 T=0.0001
ExAC Other Sub 802 C=1.000 T=0.000
The PAGE Study Global Study-wide 78612 C=0.99997 T=0.00003
The PAGE Study AfricanAmerican Sub 32458 C=0.99997 T=0.00003
The PAGE Study Mexican Sub 10810 C=0.99991 T=0.00009
The PAGE Study Asian Sub 8318 C=1.0000 T=0.0000
The PAGE Study PuertoRican Sub 7918 C=1.0000 T=0.0000
The PAGE Study NativeHawaiian Sub 4502 C=1.0000 T=0.0000
The PAGE Study Cuban Sub 4230 C=1.0000 T=0.0000
The PAGE Study Dominican Sub 3828 C=1.0000 T=0.0000
The PAGE Study CentralAmerican Sub 2450 C=1.0000 T=0.0000
The PAGE Study SouthAmerican Sub 1982 C=1.0000 T=0.0000
The PAGE Study NativeAmerican Sub 1260 C=1.0000 T=0.0000
The PAGE Study SouthAsian Sub 856 C=1.000 T=0.000
14KJPN JAPANESE Study-wide 28258 C=0.99968 T=0.00032
8.3KJPN JAPANESE Study-wide 16760 C=0.99970 T=0.00030
Genetic variation in the Estonian population Estonian Study-wide 4480 C=0.9998 T=0.0002
FINRISK Finnish from FINRISK project Study-wide 282 C=0.996 T=0.004
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 15 NC_000015.10:g.58541923C>T
GRCh37.p13 chr 15 NC_000015.9:g.58834122C>T
LIPC RefSeqGene NG_011465.2:g.114948C>T
Gene: LIPC, lipase C, hepatic type (plus strand)
Molecule type Change Amino acid[Codon] SO Term
LIPC transcript NM_000236.3:c.412C>T R [CGC] > C [TGC] Coding Sequence Variant
hepatic triacylglycerol lipase precursor NP_000227.2:p.Arg138Cys R (Arg) > C (Cys) Missense Variant
LIPC transcript variant X1 XM_005254374.5:c.448C>T R [CGC] > C [TGC] Coding Sequence Variant
hepatic triacylglycerol lipase isoform X1 XP_005254431.2:p.Arg150Cys R (Arg) > C (Cys) Missense Variant
LIPC transcript variant X2 XM_005254372.2:c.412C>T R [CGC] > C [TGC] Coding Sequence Variant
hepatic triacylglycerol lipase isoform X2 XP_005254429.1:p.Arg138Cys R (Arg) > C (Cys) Missense Variant
LIPC transcript variant X3 XM_024449916.2:c.412C>T R [CGC] > C [TGC] Coding Sequence Variant
hepatic triacylglycerol lipase isoform X2 XP_024305684.1:p.Arg138Cys R (Arg) > C (Cys) Missense Variant
LIPC transcript variant X4 XM_024449917.2:c.412C>T R [CGC] > C [TGC] Coding Sequence Variant
hepatic triacylglycerol lipase isoform X2 XP_024305685.1:p.Arg138Cys R (Arg) > C (Cys) Missense Variant
LIPC transcript variant X5 XM_006720502.5:c.271C>T R [CGC] > C [TGC] Coding Sequence Variant
hepatic triacylglycerol lipase isoform X3 XP_006720565.1:p.Arg91Cys R (Arg) > C (Cys) Missense Variant
LIPC transcript variant X6 XM_047432491.1:c.271C>T R [CGC] > C [TGC] Coding Sequence Variant
hepatic triacylglycerol lipase isoform X3 XP_047288447.1:p.Arg91Cys R (Arg) > C (Cys) Missense Variant
LIPC transcript variant X7 XM_017022176.2:c.448C>T R [CGC] > C [TGC] Coding Sequence Variant
hepatic triacylglycerol lipase isoform X4 XP_016877665.1:p.Arg150Cys R (Arg) > C (Cys) 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 C= T
GRCh38.p14 chr 15 NC_000015.10:g.58541923= NC_000015.10:g.58541923C>T
GRCh37.p13 chr 15 NC_000015.9:g.58834122= NC_000015.9:g.58834122C>T
LIPC RefSeqGene NG_011465.2:g.114948= NG_011465.2:g.114948C>T
LIPC transcript NM_000236.3:c.412= NM_000236.3:c.412C>T
LIPC transcript NM_000236.2:c.412= NM_000236.2:c.412C>T
LIPC transcript variant X1 XM_005254374.5:c.448= XM_005254374.5:c.448C>T
LIPC transcript variant X1 XM_005254374.4:c.448= XM_005254374.4:c.448C>T
LIPC transcript variant X2 XM_005254374.3:c.349= XM_005254374.3:c.349C>T
LIPC transcript variant X3 XM_005254374.2:c.349= XM_005254374.2:c.349C>T
LIPC transcript variant X3 XM_005254374.1:c.349= XM_005254374.1:c.349C>T
LIPC transcript variant X5 XM_006720502.5:c.271= XM_006720502.5:c.271C>T
LIPC transcript variant X5 XM_006720502.4:c.271= XM_006720502.4:c.271C>T
LIPC transcript variant X3 XM_006720502.3:c.271= XM_006720502.3:c.271C>T
LIPC transcript variant X3 XM_006720502.2:c.271= XM_006720502.2:c.271C>T
LIPC transcript variant X5 XM_006720502.1:c.271= XM_006720502.1:c.271C>T
LIPC transcript variant X7 XM_017022176.2:c.448= XM_017022176.2:c.448C>T
LIPC transcript variant X6 XM_017022176.1:c.448= XM_017022176.1:c.448C>T
LIPC transcript variant X3 XM_024449916.2:c.412= XM_024449916.2:c.412C>T
LIPC transcript variant X2 XM_024449916.1:c.412= XM_024449916.1:c.412C>T
LIPC transcript variant X2 XM_005254372.2:c.412= XM_005254372.2:c.412C>T
LIPC transcript variant X3 XM_005254372.1:c.412= XM_005254372.1:c.412C>T
LIPC transcript variant X4 XM_024449917.2:c.412= XM_024449917.2:c.412C>T
LIPC transcript variant X4 XM_024449917.1:c.412= XM_024449917.1:c.412C>T
LIPC transcript variant X6 XM_047432491.1:c.271= XM_047432491.1:c.271C>T
hepatic triacylglycerol lipase precursor NP_000227.2:p.Arg138= NP_000227.2:p.Arg138Cys
hepatic triacylglycerol lipase isoform X1 XP_005254431.2:p.Arg150= XP_005254431.2:p.Arg150Cys
hepatic triacylglycerol lipase isoform X3 XP_006720565.1:p.Arg91= XP_006720565.1:p.Arg91Cys
hepatic triacylglycerol lipase isoform X4 XP_016877665.1:p.Arg150= XP_016877665.1:p.Arg150Cys
hepatic triacylglycerol lipase isoform X2 XP_024305684.1:p.Arg138= XP_024305684.1:p.Arg138Cys
hepatic triacylglycerol lipase isoform X2 XP_005254429.1:p.Arg138= XP_005254429.1:p.Arg138Cys
hepatic triacylglycerol lipase isoform X2 XP_024305685.1:p.Arg138= XP_024305685.1:p.Arg138Cys
hepatic triacylglycerol lipase isoform X3 XP_047288447.1:p.Arg91= XP_047288447.1:p.Arg91Cys
hepatic triacylglycerol lipase isoform X2 XP_005254431.1:p.Arg117= XP_005254431.1:p.Arg117Cys
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, 10 Frequency submissions
No Submitter Submission ID Date (Build)
1 EXOME_CHIP ss491495317 May 04, 2012 (137)
2 ILLUMINA ss780709313 Sep 08, 2015 (146)
3 ILLUMINA ss783384050 Sep 08, 2015 (146)
4 EVA_FINRISK ss1584094360 Apr 01, 2015 (144)
5 EVA_EXAC ss1691854937 Apr 01, 2015 (144)
6 ILLUMINA ss1752165616 Sep 08, 2015 (146)
7 ILLUMINA ss1917897153 Feb 12, 2016 (147)
8 ILLUMINA ss1946395179 Feb 12, 2016 (147)
9 ILLUMINA ss1959616624 Feb 12, 2016 (147)
10 HUMAN_LONGEVITY ss2207198787 Dec 20, 2016 (150)
11 GNOMAD ss2741286107 Nov 08, 2017 (151)
12 GNOMAD ss2749316739 Nov 08, 2017 (151)
13 GNOMAD ss2935478414 Nov 08, 2017 (151)
14 AFFY ss2985042969 Nov 08, 2017 (151)
15 ILLUMINA ss3021637765 Nov 08, 2017 (151)
16 ILLUMINA ss3627372953 Oct 12, 2018 (152)
17 ILLUMINA ss3634609183 Oct 12, 2018 (152)
18 ILLUMINA ss3640316504 Oct 12, 2018 (152)
19 ILLUMINA ss3644648279 Oct 12, 2018 (152)
20 ILLUMINA ss3652038756 Oct 12, 2018 (152)
21 ILLUMINA ss3653814818 Oct 12, 2018 (152)
22 EGCUT_WGS ss3680509746 Jul 13, 2019 (153)
23 ILLUMINA ss3725503955 Jul 13, 2019 (153)
24 ILLUMINA ss3744420941 Jul 13, 2019 (153)
25 ILLUMINA ss3744909701 Jul 13, 2019 (153)
26 PAGE_CC ss3771833397 Jul 13, 2019 (153)
27 ILLUMINA ss3772408354 Jul 13, 2019 (153)
28 TOPMED ss4993156742 Apr 26, 2021 (155)
29 TOMMO_GENOMICS ss5216426027 Apr 26, 2021 (155)
30 TOMMO_GENOMICS ss5770298351 Oct 16, 2022 (156)
31 EVA ss5847745011 Oct 16, 2022 (156)
32 EVA ss5949017938 Oct 16, 2022 (156)
33 Genetic variation in the Estonian population NC_000015.9 - 58834122 Oct 12, 2018 (152)
34 ExAC NC_000015.9 - 58834122 Oct 12, 2018 (152)
35 FINRISK NC_000015.9 - 58834122 Apr 27, 2020 (154)
36 gnomAD - Genomes NC_000015.10 - 58541923 Apr 26, 2021 (155)
37 gnomAD - Exomes NC_000015.9 - 58834122 Jul 13, 2019 (153)
38 The PAGE Study NC_000015.10 - 58541923 Jul 13, 2019 (153)
39 8.3KJPN NC_000015.9 - 58834122 Apr 26, 2021 (155)
40 14KJPN NC_000015.10 - 58541923 Oct 16, 2022 (156)
41 TopMed NC_000015.10 - 58541923 Apr 26, 2021 (155)
42 ALFA NC_000015.10 - 58541923 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
26247994, 2230775, 90821, 10553254, 74395334, ss491495317, ss780709313, ss783384050, ss1584094360, ss1691854937, ss1752165616, ss1917897153, ss1946395179, ss1959616624, ss2741286107, ss2749316739, ss2935478414, ss2985042969, ss3021637765, ss3627372953, ss3634609183, ss3640316504, ss3644648279, ss3652038756, ss3653814818, ss3680509746, ss3744420941, ss3744909701, ss3772408354, ss5216426027, ss5847745011, ss5949017938 NC_000015.9:58834121:C:T NC_000015.10:58541922:C:T (self)
470535722, 1054866, 104135455, 208702402, 13722093462, ss2207198787, ss3725503955, ss3771833397, ss4993156742, ss5770298351 NC_000015.10:58541922:C:T NC_000015.10:58541922: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 rs200324727

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