Name: rs9532993
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.

rs9532993

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr13:42090481 (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>A
Variation Type: SNV Single Nucleotide Variation
Frequency: A=0.139450 (36911/264690, TOPMED)
A=0.134286 (18810/140074, GnomAD)
A=0.11491 (3247/28258, 14KJPN) (+ 17 more)
A=0.14187 (2680/18890, ALFA)
A=0.11265 (1888/16760, 8.3KJPN)
A=0.1374 (880/6404, 1000G_30x)
A=0.1368 (685/5008, 1000G)
A=0.1167 (523/4480, Estonian)
A=0.1533 (591/3854, ALSPAC)
A=0.1564 (580/3708, TWINSUK)
A=0.0836 (245/2930, KOREAN)
A=0.171 (171/998, GoNL)
A=0.143 (86/600, NorthernSweden)
A=0.151 (49/324, HapMap)
A=0.130 (28/216, Qatari)
A=0.065 (14/216, Vietnamese)
C=0.463 (75/162, SGDP_PRJ)
A=0.20 (8/40, GENOME_DK)
C=0.50 (9/18, Siberian)
A=0.50 (9/18, Siberian)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: DGKH : 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	C=0.85813	A=0.14187
European	Sub	14286	C=0.84761	A=0.15239
African	Sub	2946	C=0.9067	A=0.0933
African Others	Sub	114	C=0.930	A=0.070
African American	Sub	2832	C=0.9057	A=0.0943
Asian	Sub	112	C=0.955	A=0.045
East Asian	Sub	86	C=0.94	A=0.06
Other Asian	Sub	26	C=1.00	A=0.00
Latin American 1	Sub	146	C=0.815	A=0.185
Latin American 2	Sub	610	C=0.874	A=0.126
South Asian	Sub	98	C=0.79	A=0.21
Other	Sub	692	C=0.858	A=0.142

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	C=0.860550	A=0.139450
gnomAD - Genomes	Global	Study-wide	140074	C=0.865714	A=0.134286
gnomAD - Genomes	European	Sub	75864	C=0.84537	A=0.15463
gnomAD - Genomes	African	Sub	41972	C=0.90911	A=0.09089
gnomAD - Genomes	American	Sub	13642	C=0.84724	A=0.15276
gnomAD - Genomes	Ashkenazi Jewish	Sub	3316	C=0.8281	A=0.1719
gnomAD - Genomes	East Asian	Sub	3128	C=0.9201	A=0.0799
gnomAD - Genomes	Other	Sub	2152	C=0.8327	A=0.1673
14KJPN	JAPANESE	Study-wide	28258	C=0.88509	A=0.11491
Allele Frequency Aggregator	Total	Global	18890	C=0.85813	A=0.14187
Allele Frequency Aggregator	European	Sub	14286	C=0.84761	A=0.15239
Allele Frequency Aggregator	African	Sub	2946	C=0.9067	A=0.0933
Allele Frequency Aggregator	Other	Sub	692	C=0.858	A=0.142
Allele Frequency Aggregator	Latin American 2	Sub	610	C=0.874	A=0.126
Allele Frequency Aggregator	Latin American 1	Sub	146	C=0.815	A=0.185
Allele Frequency Aggregator	Asian	Sub	112	C=0.955	A=0.045
Allele Frequency Aggregator	South Asian	Sub	98	C=0.79	A=0.21
8.3KJPN	JAPANESE	Study-wide	16760	C=0.88735	A=0.11265
1000Genomes_30x	Global	Study-wide	6404	C=0.8626	A=0.1374
1000Genomes_30x	African	Sub	1786	C=0.9138	A=0.0862
1000Genomes_30x	Europe	Sub	1266	C=0.8310	A=0.1690
1000Genomes_30x	South Asian	Sub	1202	C=0.8095	A=0.1905
1000Genomes_30x	East Asian	Sub	1170	C=0.9026	A=0.0974
1000Genomes_30x	American	Sub	980	C=0.828	A=0.172
1000Genomes	Global	Study-wide	5008	C=0.8632	A=0.1368
1000Genomes	African	Sub	1322	C=0.9077	A=0.0923
1000Genomes	East Asian	Sub	1008	C=0.9038	A=0.0962
1000Genomes	Europe	Sub	1006	C=0.8390	A=0.1610
1000Genomes	South Asian	Sub	978	C=0.809	A=0.191
1000Genomes	American	Sub	694	C=0.831	A=0.169
Genetic variation in the Estonian population	Estonian	Study-wide	4480	C=0.8833	A=0.1167
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	C=0.8467	A=0.1533
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	C=0.8436	A=0.1564
KOREAN population from KRGDB	KOREAN	Study-wide	2930	C=0.9164	A=0.0836
Genome of the Netherlands Release 5	Genome of the Netherlands	Study-wide	998	C=0.829	A=0.171
Northern Sweden	ACPOP	Study-wide	600	C=0.857	A=0.143
HapMap	Global	Study-wide	324	C=0.849	A=0.151
HapMap	American	Sub	120	C=0.792	A=0.208
HapMap	African	Sub	116	C=0.897	A=0.103
HapMap	Asian	Sub	88	C=0.86	A=0.14
Qatari	Global	Study-wide	216	C=0.870	A=0.130
A Vietnamese Genetic Variation Database	Global	Study-wide	216	C=0.935	A=0.065
SGDP_PRJ	Global	Study-wide	162	C=0.463	A=0.537
The Danish reference pan genome	Danish	Study-wide	40	C=0.80	A=0.20
Siberian	Global	Study-wide	18	C=0.50	A=0.50

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 13	NC_000013.11:g.42090481C>A
GRCh37.p13 chr 13	NC_000013.10:g.42664617C>A
DGKH RefSeqGene	NG_029191.3:g.55446C>A

Gene: DGKH, diacylglycerol kinase eta (plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
DGKH transcript variant 3	NM_001204504.3:c.193-3698… NM_001204504.3:c.193-36982C>A	N/A	Intron Variant
DGKH transcript variant 1	NM_152910.6:c.193-36982C>A	N/A	Intron Variant
DGKH transcript variant 2	NM_178009.5:c.193-36982C>A	N/A	Intron Variant
DGKH transcript variant 4	NM_001204505.3:c.	N/A	Genic Upstream Transcript Variant
DGKH transcript variant 5	NM_001204506.3:c.	N/A	Genic Upstream Transcript Variant
DGKH transcript variant 6	NM_001297429.2:c.	N/A	Genic Upstream Transcript Variant
DGKH transcript variant 7	NR_123714.2:n.	N/A	Genic Upstream Transcript Variant
DGKH transcript variant 8	NR_123715.2:n.	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	C=	A
GRCh38.p14 chr 13	NC_000013.11:g.42090481=	NC_000013.11:g.42090481C>A
GRCh37.p13 chr 13	NC_000013.10:g.42664617=	NC_000013.10:g.42664617C>A
DGKH RefSeqGene	NG_029191.3:g.55446=	NG_029191.3:g.55446C>A
DGKH transcript variant 3	NM_001204504.1:c.193-36982=	NM_001204504.1:c.193-36982C>A
DGKH transcript variant 3	NM_001204504.3:c.193-36982=	NM_001204504.3:c.193-36982C>A
DGKH transcript variant 1	NM_152910.4:c.193-36982=	NM_152910.4:c.193-36982C>A
DGKH transcript variant 1	NM_152910.6:c.193-36982=	NM_152910.6:c.193-36982C>A
DGKH transcript variant 2	NM_178009.3:c.193-36982=	NM_178009.3:c.193-36982C>A
DGKH transcript variant 2	NM_178009.5:c.193-36982=	NM_178009.5:c.193-36982C>A
DGKH transcript variant X1	XM_005266270.1:c.193-36982=	XM_005266270.1:c.193-36982C>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#.

60 SubSNP, 19 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	SC_SNP	ss13215072	Dec 05, 2003 (119)
2	SC_SNP	ss18058474	Feb 27, 2004 (126)
3	SC_SNP	ss18064106	Feb 27, 2004 (126)
4	ABI	ss40327477	Mar 11, 2006 (126)
5	HGSV	ss82195204	Dec 14, 2007 (130)
6	HUMANGENOME_JCVI	ss97153684	Feb 03, 2009 (130)
7	BGI	ss103115542	Dec 01, 2009 (131)
8	1000GENOMES	ss112732475	Jan 25, 2009 (130)
9	BUSHMAN	ss199136219	Jul 04, 2010 (132)
10	BCM-HGSC-SUB	ss208600450	Jul 04, 2010 (132)
11	1000GENOMES	ss226155218	Jul 14, 2010 (132)
12	1000GENOMES	ss236230625	Jul 15, 2010 (132)
13	1000GENOMES	ss242730530	Jul 15, 2010 (132)
14	PJP	ss291586944	May 09, 2011 (134)
15	GMI	ss475792178	May 04, 2012 (137)
16	TISHKOFF	ss563633861	Apr 25, 2013 (138)
17	SSMP	ss659234603	Apr 25, 2013 (138)
18	EVA-GONL	ss990332141	Aug 21, 2014 (142)
19	JMKIDD_LAB	ss1079041700	Aug 21, 2014 (142)
20	1000GENOMES	ss1348000754	Aug 21, 2014 (142)
21	DDI	ss1427171353	Apr 01, 2015 (144)
22	EVA_GENOME_DK	ss1576753441	Apr 01, 2015 (144)
23	EVA_UK10K_ALSPAC	ss1630162101	Apr 01, 2015 (144)
24	EVA_UK10K_TWINSUK	ss1673156134	Apr 01, 2015 (144)
25	EVA_DECODE	ss1684853439	Apr 01, 2015 (144)
26	HAMMER_LAB	ss1807585565	Sep 08, 2015 (146)
27	WEILL_CORNELL_DGM	ss1933700337	Feb 12, 2016 (147)
28	JJLAB	ss2027608924	Sep 14, 2016 (149)
29	USC_VALOUEV	ss2155974259	Dec 20, 2016 (150)
30	HUMAN_LONGEVITY	ss2195872261	Dec 20, 2016 (150)
31	GRF	ss2700350825	Nov 08, 2017 (151)
32	GNOMAD	ss2919013098	Nov 08, 2017 (151)
33	SWEGEN	ss3010929057	Nov 08, 2017 (151)
34	BIOINF_KMB_FNS_UNIBA	ss3027621305	Nov 08, 2017 (151)
35	CSHL	ss3350428911	Nov 08, 2017 (151)
36	URBANLAB	ss3650020632	Oct 12, 2018 (152)
37	EGCUT_WGS	ss3678192013	Jul 13, 2019 (153)
38	EVA_DECODE	ss3695180121	Jul 13, 2019 (153)
39	ACPOP	ss3739698127	Jul 13, 2019 (153)
40	EVA	ss3751395097	Jul 13, 2019 (153)
41	KHV_HUMAN_GENOMES	ss3816726785	Jul 13, 2019 (153)
42	EVA	ss3833517821	Apr 27, 2020 (154)
43	EVA	ss3840339100	Apr 27, 2020 (154)
44	EVA	ss3845824547	Apr 27, 2020 (154)
45	SGDP_PRJ	ss3879859496	Apr 27, 2020 (154)
46	KRGDB	ss3928699696	Apr 27, 2020 (154)
47	TOPMED	ss4944321045	Apr 27, 2021 (155)
48	TOMMO_GENOMICS	ss5209741646	Apr 27, 2021 (155)
49	1000G_HIGH_COVERAGE	ss5293540319	Oct 16, 2022 (156)
50	EVA	ss5410413646	Oct 16, 2022 (156)
51	HUGCELL_USP	ss5487922591	Oct 16, 2022 (156)
52	EVA	ss5510952492	Oct 16, 2022 (156)
53	1000G_HIGH_COVERAGE	ss5592392083	Oct 16, 2022 (156)
54	SANFORD_IMAGENETICS	ss5654658437	Oct 16, 2022 (156)
55	TOMMO_GENOMICS	ss5761544214	Oct 16, 2022 (156)
56	YY_MCH	ss5814062204	Oct 16, 2022 (156)
57	EVA	ss5839398709	Oct 16, 2022 (156)
58	EVA	ss5924884008	Oct 16, 2022 (156)
59	EVA	ss5946073970	Oct 16, 2022 (156)
60	EVA	ss5980788614	Oct 16, 2022 (156)
61	1000Genomes	NC_000013.10 - 42664617	Oct 12, 2018 (152)
62	1000Genomes_30x	NC_000013.11 - 42090481	Oct 16, 2022 (156)
63	The Avon Longitudinal Study of Parents and Children	NC_000013.10 - 42664617	Oct 12, 2018 (152)
64	Genetic variation in the Estonian population	NC_000013.10 - 42664617	Oct 12, 2018 (152)
65	The Danish reference pan genome	NC_000013.10 - 42664617	Apr 27, 2020 (154)
66	gnomAD - Genomes	NC_000013.11 - 42090481	Apr 27, 2021 (155)
67	Genome of the Netherlands Release 5	NC_000013.10 - 42664617	Apr 27, 2020 (154)
68	HapMap	NC_000013.11 - 42090481	Apr 27, 2020 (154)
69	KOREAN population from KRGDB	NC_000013.10 - 42664617	Apr 27, 2020 (154)
70	Northern Sweden	NC_000013.10 - 42664617	Jul 13, 2019 (153)
71	Qatari	NC_000013.10 - 42664617	Apr 27, 2020 (154)
72	SGDP_PRJ	NC_000013.10 - 42664617	Apr 27, 2020 (154)
73	Siberian	NC_000013.10 - 42664617	Apr 27, 2020 (154)
74	8.3KJPN	NC_000013.10 - 42664617	Apr 27, 2021 (155)
75	14KJPN	NC_000013.11 - 42090481	Oct 16, 2022 (156)
76	TopMed	NC_000013.11 - 42090481	Apr 27, 2021 (155)
77	UK 10K study - Twins	NC_000013.10 - 42664617	Oct 12, 2018 (152)
78	A Vietnamese Genetic Variation Database	NC_000013.10 - 42664617	Jul 13, 2019 (153)
79	ALFA	NC_000013.11 - 42090481	Apr 27, 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).

Associated ID	History Updated (Build)
rs11147868	Mar 11, 2006 (126)
rs57041134	May 23, 2008 (130)

Added to this RefSNP Cluster:

Submission IDs	Observation SPDI	Canonical SPDI	Source RSIDs
ss82195204, ss112732475, ss199136219, ss208600450, ss291586944, ss475792178, ss1684853439	NC_000013.9:41562616:C:A	NC_000013.11:42090480:C:A	(self)
60863628, 33809405, 23930261, 3276151, 15086249, 35877090, 12982992, 15742267, 31876476, 8490613, 67710953, 33809405, 7501328, ss226155218, ss236230625, ss242730530, ss563633861, ss659234603, ss990332141, ss1079041700, ss1348000754, ss1427171353, ss1576753441, ss1630162101, ss1673156134, ss1807585565, ss1933700337, ss2027608924, ss2155974259, ss2700350825, ss2919013098, ss3010929057, ss3350428911, ss3678192013, ss3739698127, ss3751395097, ss3833517821, ss3840339100, ss3879859496, ss3928699696, ss5209741646, ss5410413646, ss5510952492, ss5654658437, ss5839398709, ss5946073970, ss5980788614	NC_000013.10:42664616:C:A	NC_000013.11:42090480:C:A	(self)
79918018, 429109837, 978122, 95381318, 159866703, 597502137, ss2195872261, ss3027621305, ss3650020632, ss3695180121, ss3816726785, ss3845824547, ss4944321045, ss5293540319, ss5487922591, ss5592392083, ss5761544214, ss5814062204, ss5924884008	NC_000013.11:42090480:C:A	NC_000013.11:42090480:C:A	(self)
ss13215072	NT_024524.12:11239107:C:A	NC_000013.11:42090480:C:A	(self)
ss18058474, ss18064106, ss40327477, ss97153684, ss103115542	NT_024524.14:23644616:C:A	NC_000013.11:42090480:C: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 rs9532993

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

rs9532993