Name: rs117338748
Published: September 21, 2022
License: Open Access

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.

rs117338748

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr15:58422040 (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=0.015410 (4079/264690, TOPMED)
A=0.016033 (2248/140212, GnomAD)
A=0.01611 (1363/84624, ALFA) (+ 13 more)
A=0.0091 (58/6404, 1000G_30x)
A=0.0084 (42/5008, 1000G)
A=0.0076 (34/4480, Estonian)
A=0.0202 (78/3854, ALSPAC)
A=0.0191 (71/3708, TWINSUK)
A=0.022 (22/998, GoNL)
A=0.017 (10/600, NorthernSweden)
A=0.023 (5/216, Qatari)
A=0.03 (1/40, GENOME_DK)
G=0.5 (3/6, SGDP_PRJ)
A=0.5 (3/6, SGDP_PRJ)
G=0.5 (2/4, Siberian)
A=0.5 (2/4, Siberian)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: LIPC : 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	84624	G=0.98389	A=0.01611
European	Sub	73990	G=0.98325	A=0.01675
African	Sub	3770	G=0.9830	A=0.0170
African Others	Sub	166	G=0.982	A=0.018
African American	Sub	3604	G=0.9831	A=0.0169
Asian	Sub	3278	G=0.9969	A=0.0031
East Asian	Sub	2650	G=1.0000	A=0.0000
Other Asian	Sub	628	G=0.984	A=0.016
Latin American 1	Sub	444	G=0.984	A=0.016
Latin American 2	Sub	934	G=0.989	A=0.011
South Asian	Sub	274	G=0.993	A=0.007
Other	Sub	1934	G=0.9840	A=0.0160

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
TopMed	Global	Study-wide	264690	G=0.984590	A=0.015410
gnomAD - Genomes	Global	Study-wide	140212	G=0.983967	A=0.016033
gnomAD - Genomes	European	Sub	75920	G=0.98321	A=0.01679
gnomAD - Genomes	African	Sub	42028	G=0.98104	A=0.01896
gnomAD - Genomes	American	Sub	13656	G=0.99290	A=0.00710
gnomAD - Genomes	Ashkenazi Jewish	Sub	3322	G=0.9895	A=0.0105
gnomAD - Genomes	East Asian	Sub	3132	G=0.9997	A=0.0003
gnomAD - Genomes	Other	Sub	2154	G=0.9800	A=0.0200
Allele Frequency Aggregator	Total	Global	84624	G=0.98389	A=0.01611
Allele Frequency Aggregator	European	Sub	73990	G=0.98325	A=0.01675
Allele Frequency Aggregator	African	Sub	3770	G=0.9830	A=0.0170
Allele Frequency Aggregator	Asian	Sub	3278	G=0.9969	A=0.0031
Allele Frequency Aggregator	Other	Sub	1934	G=0.9840	A=0.0160
Allele Frequency Aggregator	Latin American 2	Sub	934	G=0.989	A=0.011
Allele Frequency Aggregator	Latin American 1	Sub	444	G=0.984	A=0.016
Allele Frequency Aggregator	South Asian	Sub	274	G=0.993	A=0.007
1000Genomes_30x	Global	Study-wide	6404	G=0.9909	A=0.0091
1000Genomes_30x	African	Sub	1786	G=0.9866	A=0.0134
1000Genomes_30x	Europe	Sub	1266	G=0.9882	A=0.0118
1000Genomes_30x	South Asian	Sub	1202	G=0.9900	A=0.0100
1000Genomes_30x	East Asian	Sub	1170	G=1.0000	A=0.0000
1000Genomes_30x	American	Sub	980	G=0.993	A=0.007
1000Genomes	Global	Study-wide	5008	G=0.9916	A=0.0084
1000Genomes	African	Sub	1322	G=0.9864	A=0.0136
1000Genomes	East Asian	Sub	1008	G=0.9990	A=0.0010
1000Genomes	Europe	Sub	1006	G=0.9920	A=0.0080
1000Genomes	South Asian	Sub	978	G=0.989	A=0.011
1000Genomes	American	Sub	694	G=0.994	A=0.006
Genetic variation in the Estonian population	Estonian	Study-wide	4480	G=0.9924	A=0.0076
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	G=0.9798	A=0.0202
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	G=0.9809	A=0.0191
Genome of the Netherlands Release 5	Genome of the Netherlands	Study-wide	998	G=0.978	A=0.022
Northern Sweden	ACPOP	Study-wide	600	G=0.983	A=0.017
Qatari	Global	Study-wide	216	G=0.977	A=0.023
The Danish reference pan genome	Danish	Study-wide	40	G=0.97	A=0.03
SGDP_PRJ	Global	Study-wide	6	G=0.5	A=0.5
Siberian	Global	Study-wide	4	G=0.5	A=0.5

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.58422040G>A
GRCh37.p13 chr 15	NC_000015.9:g.58714239G>A

Gene: LIPC, lipase C, hepatic type (plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
LIPC transcript	NM_000236.3:c.	N/A	Genic Upstream Transcript Variant
LIPC transcript variant X2	XM_005254372.2:c.-40-9953… XM_005254372.2:c.-40-9953G>A	N/A	Intron Variant
LIPC transcript variant X3	XM_024449916.2:c.-365-878… XM_024449916.2:c.-365-8787G>A	N/A	Intron Variant
LIPC transcript variant X1	XM_005254374.5:c.	N/A	Genic Upstream Transcript Variant
LIPC transcript variant X5	XM_006720502.5:c.	N/A	Genic Upstream Transcript Variant
LIPC transcript variant X7	XM_017022176.2:c.	N/A	Genic Upstream Transcript Variant
LIPC transcript variant X4	XM_024449917.2:c.	N/A	Genic Upstream Transcript Variant
LIPC transcript variant X6	XM_047432491.1:c.	N/A	Genic Upstream Transcript Variant

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

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 15	NC_000015.10:g.58422040=	NC_000015.10:g.58422040G>A
GRCh37.p13 chr 15	NC_000015.9:g.58714239=	NC_000015.9:g.58714239G>A
LIPC transcript variant X3	XM_005254372.1:c.-40-9953=	XM_005254372.1:c.-40-9953G>A
LIPC transcript variant X2	XM_005254372.2:c.-40-9953=	XM_005254372.2:c.-40-9953G>A
LIPC transcript variant X2	XM_005254373.1:c.-40-9953=	XM_005254373.1:c.-40-9953G>A
LIPC transcript variant X3	XM_024449916.2:c.-365-8787=	XM_024449916.2:c.-365-8787G>A

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#.

34 SubSNP, 14 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	1000GENOMES	ss236797425	Jul 15, 2010 (132)
2	ILLUMINA	ss535280269	Sep 08, 2015 (146)
3	TISHKOFF	ss564510883	Apr 25, 2013 (138)
4	SSMP	ss660240977	Apr 25, 2013 (138)
5	EVA-GONL	ss991838189	Aug 21, 2014 (142)
6	JMKIDD_LAB	ss1080166418	Aug 21, 2014 (142)
7	1000GENOMES	ss1353663222	Aug 21, 2014 (142)
8	EVA_GENOME_DK	ss1577647601	Apr 01, 2015 (144)
9	EVA_UK10K_ALSPAC	ss1633103477	Apr 01, 2015 (144)
10	EVA_UK10K_TWINSUK	ss1676097510	Apr 01, 2015 (144)
11	EVA_DECODE	ss1695857915	Apr 01, 2015 (144)
12	WEILL_CORNELL_DGM	ss1935244167	Feb 12, 2016 (147)
13	JJLAB	ss2028402489	Sep 14, 2016 (149)
14	USC_VALOUEV	ss2156806337	Dec 20, 2016 (150)
15	HUMAN_LONGEVITY	ss2207190251	Dec 20, 2016 (150)
16	GNOMAD	ss2935467404	Nov 08, 2017 (151)
17	SWEGEN	ss3013363935	Nov 08, 2017 (151)
18	CSHL	ss3351139017	Nov 08, 2017 (151)
19	ILLUMINA	ss3627372594	Oct 12, 2018 (152)
20	EGCUT_WGS	ss3680508193	Jul 13, 2019 (153)
21	EVA_DECODE	ss3697988864	Jul 13, 2019 (153)
22	ACPOP	ss3740967779	Jul 13, 2019 (153)
23	KHV_HUMAN_GENOMES	ss3818465533	Jul 13, 2019 (153)
24	EVA	ss3834260937	Apr 27, 2020 (154)
25	SGDP_PRJ	ss3883021951	Apr 27, 2020 (154)
26	TOPMED	ss4993121725	Apr 26, 2021 (155)
27	1000G_HIGH_COVERAGE	ss5298615963	Oct 16, 2022 (156)
28	EVA	ss5419549757	Oct 16, 2022 (156)
29	HUGCELL_USP	ss5492325340	Oct 16, 2022 (156)
30	1000G_HIGH_COVERAGE	ss5600106642	Oct 16, 2022 (156)
31	SANFORD_IMAGENETICS	ss5657611439	Oct 16, 2022 (156)
32	EVA	ss5828269186	Oct 16, 2022 (156)
33	EVA	ss5876076498	Oct 16, 2022 (156)
34	EVA	ss5949015858	Oct 16, 2022 (156)
35	1000Genomes	NC_000015.9 - 58714239	Oct 12, 2018 (152)
36	1000Genomes_30x	NC_000015.10 - 58422040	Oct 16, 2022 (156)
37	The Avon Longitudinal Study of Parents and Children	NC_000015.9 - 58714239	Oct 12, 2018 (152)
38	Genetic variation in the Estonian population	NC_000015.9 - 58714239	Oct 12, 2018 (152)
39	The Danish reference pan genome	NC_000015.9 - 58714239	Apr 27, 2020 (154)
40	gnomAD - Genomes	NC_000015.10 - 58422040	Apr 26, 2021 (155)
41	Genome of the Netherlands Release 5	NC_000015.9 - 58714239	Apr 27, 2020 (154)
42	Northern Sweden	NC_000015.9 - 58714239	Jul 13, 2019 (153)
43	Qatari	NC_000015.9 - 58714239	Apr 27, 2020 (154)
44	SGDP_PRJ	NC_000015.9 - 58714239	Apr 27, 2020 (154)
45	Siberian	NC_000015.9 - 58714239	Apr 27, 2020 (154)
46	TopMed	NC_000015.10 - 58422040	Apr 26, 2021 (155)
47	UK 10K study - Twins	NC_000015.9 - 58714239	Oct 12, 2018 (152)
48	ALFA	NC_000015.10 - 58422040	Apr 26, 2021 (155)

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
ss1695857915	NC_000015.8:56501530:G:A	NC_000015.10:58422039:G:A	(self)
66742139, 37052198, 26246441, 3878220, 16545334, 14252644, 17286097, 35038931, 9322691, 37052198, ss236797425, ss535280269, ss564510883, ss660240977, ss991838189, ss1080166418, ss1353663222, ss1577647601, ss1633103477, ss1676097510, ss1935244167, ss2028402489, ss2156806337, ss2935467404, ss3013363935, ss3351139017, ss3627372594, ss3680508193, ss3740967779, ss3834260937, ss3883021951, ss5419549757, ss5657611439, ss5828269186, ss5949015858	NC_000015.9:58714238:G:A	NC_000015.10:58422039:G:A	(self)
87632577, 470507561, 208667385, 3349641722, ss2207190251, ss3697988864, ss3818465533, ss4993121725, ss5298615963, ss5492325340, ss5600106642, ss5876076498	NC_000015.10:58422039:G:A	NC_000015.10:58422039:G:A	(self)

Publications tab displays PubMed articles citing the variation as a listing of PMID, Title, Author, Year, Journal, ordered by Year, descending.

No publications for rs117338748

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.

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dbSNP Short Genetic Variations

Welcome to the Reference SNP (rs) Report

Reference SNP (rs) Report

rs117338748