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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.

rs375790

Current Build 155

Released April 9, 2021

Organism
Homo sapiens
Position
chr10:88751954 (GRCh38.p13) 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>A / T>C / T>G
Variation Type
SNV Single Nucleotide Variation
Frequency
G=0.248177 (65690/264690, TOPMED)
G=0.36778 (6164/16760, 8.3KJPN)
G=0.11282 (1574/13952, ALFA) (+ 14 more)
G=0.2712 (1358/5008, 1000G)
G=0.2210 (990/4480, Estonian)
G=0.2107 (812/3854, ALSPAC)
G=0.2260 (838/3708, TWINSUK)
G=0.4126 (1209/2930, KOREAN)
G=0.221 (221/998, GoNL)
G=0.197 (118/600, NorthernSweden)
T=0.403 (108/268, SGDP_PRJ)
G=0.227 (49/216, Qatari)
G=0.383 (82/214, Vietnamese)
G=0.22 (14/64, Ancient Sardinia)
G=0.23 (9/40, GENOME_DK)
T=0.50 (8/16, Siberian)
G=0.50 (8/16, Siberian)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
LIPK : 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.p13 chr 10 NC_000010.11:g.88751954T>A
GRCh38.p13 chr 10 NC_000010.11:g.88751954T>C
GRCh38.p13 chr 10 NC_000010.11:g.88751954T>G
GRCh37.p13 chr 10 NC_000010.10:g.90511711T>A
GRCh37.p13 chr 10 NC_000010.10:g.90511711T>C
GRCh37.p13 chr 10 NC_000010.10:g.90511711T>G
Gene: LIPK, lipase family member K (plus strand)
Molecule type Change Amino acid[Codon] SO Term
LIPK transcript variant 1 NM_001080518.2:c.961-563T…

NM_001080518.2:c.961-563T>A

N/A Intron Variant
LIPK transcript variant 2 NM_001378091.1:c.862-563T…

NM_001378091.1:c.862-563T>A

N/A Intron Variant
LIPK transcript variant X1 XM_011540073.3:c.1021-563…

XM_011540073.3:c.1021-563T>A

N/A Intron Variant
LIPK transcript variant X2 XM_011540075.1:c.988-563T…

XM_011540075.1:c.988-563T>A

N/A Intron Variant
LIPK transcript variant X9 XM_011540082.1:c.559-563T…

XM_011540082.1:c.559-563T>A

N/A Intron Variant
LIPK transcript variant X4 XM_017016545.1:c.949-563T…

XM_017016545.1:c.949-563T>A

N/A Intron Variant
LIPK transcript variant X5 XM_017016546.2:c.922-563T…

XM_017016546.2:c.922-563T>A

N/A Intron Variant
LIPK transcript variant X6 XM_017016547.2:c.874-563T…

XM_017016547.2:c.874-563T>A

N/A Intron Variant
LIPK transcript variant X7 XM_017016548.2:c. N/A Genic Downstream Transcript Variant
LIPK transcript variant X8 XR_001747183.2:n. N/A Intron Variant
LIPK transcript variant X10 XR_001747184.2:n. N/A Genic Downstream 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

ALFA Allele Frequency (New)
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: 20201027095038
Population Group Sample Size Ref Allele Alt Allele
Total Global 13952 T=0.88718 C=0.00000, G=0.11282
European Sub 11284 T=0.86893 C=0.00000, G=0.13107
African Sub 1684 T=0.9739 C=0.0000, G=0.0261
African Others Sub 66 T=0.97 C=0.00, G=0.03
African American Sub 1618 T=0.9740 C=0.0000, G=0.0260
Asian Sub 40 T=1.00 C=0.00, G=0.00
East Asian Sub 32 T=1.00 C=0.00, G=0.00
Other Asian Sub 8 T=1.0 C=0.0, G=0.0
Latin American 1 Sub 92 T=1.00 C=0.00, G=0.00
Latin American 2 Sub 334 T=1.000 C=0.000, G=0.000
South Asian Sub 48 T=0.98 C=0.00, G=0.02
Other Sub 470 T=0.894 C=0.000, G=0.106


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=0.751823 G=0.248177
8.3KJPN JAPANESE Study-wide 16760 T=0.63222 G=0.36778
1000Genomes Global Study-wide 5008 T=0.7288 G=0.2712
1000Genomes African Sub 1322 T=0.7564 G=0.2436
1000Genomes East Asian Sub 1008 T=0.6498 G=0.3502
1000Genomes Europe Sub 1006 T=0.7783 G=0.2217
1000Genomes South Asian Sub 978 T=0.739 G=0.261
1000Genomes American Sub 694 T=0.705 G=0.295
Genetic variation in the Estonian population Estonian Study-wide 4480 T=0.7790 G=0.2210
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 T=0.7893 G=0.2107
UK 10K study - Twins TWIN COHORT Study-wide 3708 T=0.7740 G=0.2260
KOREAN population from KRGDB KOREAN Study-wide 2930 T=0.5874 A=0.0000, G=0.4126
Genome of the Netherlands Release 5 Genome of the Netherlands Study-wide 998 T=0.779 G=0.221
Northern Sweden ACPOP Study-wide 600 T=0.803 G=0.197
SGDP_PRJ Global Study-wide 268 T=0.403 G=0.597
Qatari Global Study-wide 216 T=0.773 G=0.227
A Vietnamese Genetic Variation Database Global Study-wide 214 T=0.617 G=0.383
Ancient Sardinia genome-wide 1240k capture data generation and analysis Global Study-wide 64 T=0.78 G=0.22
The Danish reference pan genome Danish Study-wide 40 T=0.78 G=0.23
Siberian Global Study-wide 16 T=0.50 G=0.50
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= A C G
GRCh38.p13 chr 10 NC_000010.11:g.88751954= NC_000010.11:g.88751954T>A NC_000010.11:g.88751954T>C NC_000010.11:g.88751954T>G
GRCh37.p13 chr 10 NC_000010.10:g.90511711= NC_000010.10:g.90511711T>A NC_000010.10:g.90511711T>C NC_000010.10:g.90511711T>G
LIPK transcript NM_001080518.1:c.961-563= NM_001080518.1:c.961-563T>A NM_001080518.1:c.961-563T>C NM_001080518.1:c.961-563T>G
LIPK transcript variant 1 NM_001080518.2:c.961-563= NM_001080518.2:c.961-563T>A NM_001080518.2:c.961-563T>C NM_001080518.2:c.961-563T>G
LIPK transcript variant 2 NM_001378091.1:c.862-563= NM_001378091.1:c.862-563T>A NM_001378091.1:c.862-563T>C NM_001378091.1:c.862-563T>G
LIPK transcript variant X1 XM_011540073.3:c.1021-563= XM_011540073.3:c.1021-563T>A XM_011540073.3:c.1021-563T>C XM_011540073.3:c.1021-563T>G
LIPK transcript variant X2 XM_011540075.1:c.988-563= XM_011540075.1:c.988-563T>A XM_011540075.1:c.988-563T>C XM_011540075.1:c.988-563T>G
LIPK transcript variant X9 XM_011540082.1:c.559-563= XM_011540082.1:c.559-563T>A XM_011540082.1:c.559-563T>C XM_011540082.1:c.559-563T>G
LIPK transcript variant X4 XM_017016545.1:c.949-563= XM_017016545.1:c.949-563T>A XM_017016545.1:c.949-563T>C XM_017016545.1:c.949-563T>G
LIPK transcript variant X5 XM_017016546.2:c.922-563= XM_017016546.2:c.922-563T>A XM_017016546.2:c.922-563T>C XM_017016546.2:c.922-563T>G
LIPK transcript variant X6 XM_017016547.2:c.874-563= XM_017016547.2:c.874-563T>A XM_017016547.2:c.874-563T>C XM_017016547.2:c.874-563T>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#.

53 SubSNP, 18 Frequency submissions
No Submitter Submission ID Date (Build)
1 SC_JCM ss480496 Jul 16, 2000 (80)
2 KWOK ss1764668 Oct 18, 2000 (87)
3 WI_SSAHASNP ss6823584 Feb 20, 2003 (111)
4 ABI ss39792597 Mar 15, 2006 (126)
5 HUMANGENOME_JCVI ss97672103 Feb 06, 2009 (130)
6 1000GENOMES ss109638465 Jan 24, 2009 (130)
7 ILLUMINA-UK ss119259539 Feb 15, 2009 (130)
8 ENSEMBL ss137900129 Dec 01, 2009 (131)
9 COMPLETE_GENOMICS ss174681751 Jul 04, 2010 (132)
10 BCM-HGSC-SUB ss207193992 Jul 04, 2010 (132)
11 1000GENOMES ss224863006 Jul 14, 2010 (132)
12 1000GENOMES ss235276517 Jul 15, 2010 (132)
13 1000GENOMES ss241963477 Jul 15, 2010 (132)
14 BL ss254500069 May 09, 2011 (134)
15 GMI ss280716868 May 04, 2012 (137)
16 PJP ss290891273 May 09, 2011 (134)
17 TISHKOFF ss562118049 Apr 25, 2013 (138)
18 SSMP ss657130636 Apr 25, 2013 (138)
19 EVA-GONL ss987760120 Aug 21, 2014 (142)
20 JMKIDD_LAB ss1077184459 Aug 21, 2014 (142)
21 1000GENOMES ss1338459862 Aug 21, 2014 (142)
22 DDI ss1426398986 Apr 01, 2015 (144)
23 EVA_GENOME_DK ss1575272335 Apr 01, 2015 (144)
24 EVA_DECODE ss1597433082 Apr 01, 2015 (144)
25 EVA_UK10K_ALSPAC ss1625106468 Apr 01, 2015 (144)
26 EVA_UK10K_TWINSUK ss1668100501 Apr 01, 2015 (144)
27 HAMMER_LAB ss1806502940 Sep 08, 2015 (146)
28 WEILL_CORNELL_DGM ss1931127930 Feb 12, 2016 (147)
29 GENOMED ss1967190451 Jul 19, 2016 (147)
30 JJLAB ss2026291837 Sep 14, 2016 (149)
31 USC_VALOUEV ss2154567223 Dec 20, 2016 (150)
32 HUMAN_LONGEVITY ss2176811390 Dec 20, 2016 (150)
33 TOPMED ss2339915417 Dec 20, 2016 (150)
34 SYSTEMSBIOZJU ss2627615018 Nov 08, 2017 (151)
35 GRF ss2698819061 Nov 08, 2017 (151)
36 GNOMAD ss2891664634 Nov 08, 2017 (151)
37 SWEGEN ss3006897980 Nov 08, 2017 (151)
38 BIOINF_KMB_FNS_UNIBA ss3026935505 Nov 08, 2017 (151)
39 TOPMED ss3126453098 Nov 08, 2017 (151)
40 TOPMED ss3126453099 Nov 08, 2017 (151)
41 CSHL ss3349242565 Nov 08, 2017 (151)
42 URBANLAB ss3649432359 Oct 12, 2018 (152)
43 EGCUT_WGS ss3674308401 Jul 13, 2019 (153)
44 EVA_DECODE ss3690379816 Jul 13, 2019 (153)
45 ACPOP ss3737548509 Jul 13, 2019 (153)
46 EVA ss3748418708 Jul 13, 2019 (153)
47 KHV_HUMAN_GENOMES ss3813785335 Jul 13, 2019 (153)
48 EVA ss3832255294 Apr 26, 2020 (154)
49 SGDP_PRJ ss3874743813 Apr 26, 2020 (154)
50 KRGDB ss3922860912 Apr 26, 2020 (154)
51 EVA ss3985490740 Apr 26, 2021 (155)
52 TOPMED ss4861201265 Apr 26, 2021 (155)
53 TOMMO_GENOMICS ss5198785339 Apr 26, 2021 (155)
54 1000Genomes NC_000010.10 - 90511711 Oct 12, 2018 (152)
55 The Avon Longitudinal Study of Parents and Children NC_000010.10 - 90511711 Oct 12, 2018 (152)
56 Genetic variation in the Estonian population NC_000010.10 - 90511711 Oct 12, 2018 (152)
57 The Danish reference pan genome NC_000010.10 - 90511711 Apr 26, 2020 (154)
58 gnomAD - Genomes

Submission ignored due to conflicting rows:
Row 359548493 (NC_000010.11:88751953:T:C 37/140068)
Row 359548494 (NC_000010.11:88751953:T:G 33036/139998)

- Apr 26, 2021 (155)
59 gnomAD - Genomes

Submission ignored due to conflicting rows:
Row 359548493 (NC_000010.11:88751953:T:C 37/140068)
Row 359548494 (NC_000010.11:88751953:T:G 33036/139998)

- Apr 26, 2021 (155)
60 Genome of the Netherlands Release 5 NC_000010.10 - 90511711 Apr 26, 2020 (154)
61 KOREAN population from KRGDB NC_000010.10 - 90511711 Apr 26, 2020 (154)
62 Northern Sweden NC_000010.10 - 90511711 Jul 13, 2019 (153)
63 Ancient Sardinia genome-wide 1240k capture data generation and analysis NC_000010.10 - 90511711 Apr 26, 2021 (155)
64 Qatari NC_000010.10 - 90511711 Apr 26, 2020 (154)
65 SGDP_PRJ NC_000010.10 - 90511711 Apr 26, 2020 (154)
66 Siberian NC_000010.10 - 90511711 Apr 26, 2020 (154)
67 8.3KJPN NC_000010.10 - 90511711 Apr 26, 2021 (155)
68 TopMed NC_000010.11 - 88751954 Apr 26, 2021 (155)
69 UK 10K study - Twins NC_000010.10 - 90511711 Oct 12, 2018 (152)
70 A Vietnamese Genetic Variation Database NC_000010.10 - 90511711 Jul 13, 2019 (153)
71 ALFA NC_000010.11 - 88751954 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
30038306, ss3922860912 NC_000010.10:90511710:T:A NC_000010.11:88751953:T:A (self)
ss2891664634 NC_000010.10:90511710:T:C NC_000010.11:88751953:T:C (self)
10345673895, ss2176811390, ss3126453098 NC_000010.11:88751953:T:C NC_000010.11:88751953:T:C (self)
ss109638465, ss119259539, ss174681751, ss207193992, ss254500069, ss280716868, ss290891273, ss1597433082 NC_000010.9:90501690:T:G NC_000010.11:88751953:T:G (self)
50884994, 28246640, 20046649, 2265862, 12596031, 30038306, 10833374, 716667, 13169860, 26760793, 7083577, 56754646, 28246640, 6273139, ss224863006, ss235276517, ss241963477, ss562118049, ss657130636, ss987760120, ss1077184459, ss1338459862, ss1426398986, ss1575272335, ss1625106468, ss1668100501, ss1806502940, ss1931127930, ss1967190451, ss2026291837, ss2154567223, ss2339915417, ss2627615018, ss2698819061, ss2891664634, ss3006897980, ss3349242565, ss3674308401, ss3737548509, ss3748418708, ss3832255294, ss3874743813, ss3922860912, ss3985490740, ss5198785339 NC_000010.10:90511710:T:G NC_000010.11:88751953:T:G (self)
48245035, 76746920, 10345673895, ss2176811390, ss3026935505, ss3126453099, ss3649432359, ss3690379816, ss3813785335, ss4861201265 NC_000010.11:88751953:T:G NC_000010.11:88751953:T:G (self)
ss480496, ss1764668, ss6823584, ss39792597, ss97672103, ss137900129 NT_030059.13:41316174:T:G NC_000010.11:88751953:T:G (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 rs375790

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.post596+ae089ad