Name: rs12677439
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.

rs12677439

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr8:41615326 (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>G / C>T
Variation Type: SNV Single Nucleotide Variation
Frequency: T=0.234837 (62159/264690, TOPMED)
T=0.231766 (32438/139960, GnomAD)
T=0.29733 (8402/28258, 14KJPN) (+ 19 more)
T=0.22564 (6036/26750, ALFA)
T=0.29916 (5014/16760, 8.3KJPN)
T=0.2330 (1492/6404, 1000G_30x)
T=0.2372 (1188/5008, 1000G)
T=0.2134 (956/4480, Estonian)
T=0.2460 (948/3854, ALSPAC)
T=0.2414 (895/3708, TWINSUK)
T=0.2805 (822/2930, KOREAN)
T=0.2466 (465/1886, HapMap)
T=0.2429 (275/1132, Daghestan)
T=0.240 (240/998, GoNL)
T=0.147 (92/626, Chileans)
T=0.172 (103/600, NorthernSweden)
C=0.468 (118/252, SGDP_PRJ)
T=0.292 (63/216, Qatari)
T=0.306 (66/216, Vietnamese)
T=0.33 (26/80, Ancient Sardinia)
T=0.10 (4/40, GENOME_DK)
C=0.45 (9/20, Siberian)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: GPAT4 : 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	26750	C=0.77436	T=0.22564
European	Sub	15748	C=0.76518	T=0.23482
African	Sub	6260	C=0.7652	T=0.2348
African Others	Sub	210	C=0.748	T=0.252
African American	Sub	6050	C=0.7658	T=0.2342
Asian	Sub	162	C=0.673	T=0.327
East Asian	Sub	104	C=0.644	T=0.356
Other Asian	Sub	58	C=0.72	T=0.28
Latin American 1	Sub	292	C=0.774	T=0.226
Latin American 2	Sub	2766	C=0.8413	T=0.1587
South Asian	Sub	112	C=0.804	T=0.196
Other	Sub	1410	C=0.7957	T=0.2043

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=0.765163	T=0.234837
gnomAD - Genomes	Global	Study-wide	139960	C=0.768234	T=0.231766
gnomAD - Genomes	European	Sub	75824	C=0.76825	T=0.23175
gnomAD - Genomes	African	Sub	41914	C=0.76748	T=0.23252
gnomAD - Genomes	American	Sub	13632	C=0.79710	T=0.20290
gnomAD - Genomes	Ashkenazi Jewish	Sub	3324	C=0.7148	T=0.2852
gnomAD - Genomes	East Asian	Sub	3118	C=0.7075	T=0.2925
gnomAD - Genomes	Other	Sub	2148	C=0.7700	T=0.2300
14KJPN	JAPANESE	Study-wide	28258	C=0.70267	T=0.29733
Allele Frequency Aggregator	Total	Global	26750	C=0.77436	T=0.22564
Allele Frequency Aggregator	European	Sub	15748	C=0.76518	T=0.23482
Allele Frequency Aggregator	African	Sub	6260	C=0.7652	T=0.2348
Allele Frequency Aggregator	Latin American 2	Sub	2766	C=0.8413	T=0.1587
Allele Frequency Aggregator	Other	Sub	1410	C=0.7957	T=0.2043
Allele Frequency Aggregator	Latin American 1	Sub	292	C=0.774	T=0.226
Allele Frequency Aggregator	Asian	Sub	162	C=0.673	T=0.327
Allele Frequency Aggregator	South Asian	Sub	112	C=0.804	T=0.196
8.3KJPN	JAPANESE	Study-wide	16760	C=0.70084	T=0.29916
1000Genomes_30x	Global	Study-wide	6404	C=0.7670	T=0.2330
1000Genomes_30x	African	Sub	1786	C=0.7648	T=0.2352
1000Genomes_30x	Europe	Sub	1266	C=0.7425	T=0.2575
1000Genomes_30x	South Asian	Sub	1202	C=0.8153	T=0.1847
1000Genomes_30x	East Asian	Sub	1170	C=0.7111	T=0.2889
1000Genomes_30x	American	Sub	980	C=0.810	T=0.190
1000Genomes	Global	Study-wide	5008	C=0.7628	T=0.2372
1000Genomes	African	Sub	1322	C=0.7632	T=0.2368
1000Genomes	East Asian	Sub	1008	C=0.7093	T=0.2907
1000Genomes	Europe	Sub	1006	C=0.7445	T=0.2555
1000Genomes	South Asian	Sub	978	C=0.804	T=0.196
1000Genomes	American	Sub	694	C=0.808	T=0.192
Genetic variation in the Estonian population	Estonian	Study-wide	4480	C=0.7866	T=0.2134
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	C=0.7540	T=0.2460
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	C=0.7586	T=0.2414
KOREAN population from KRGDB	KOREAN	Study-wide	2930	C=0.7195	G=0.0000, T=0.2805
HapMap	Global	Study-wide	1886	C=0.7534	T=0.2466
HapMap	American	Sub	768	C=0.737	T=0.263
HapMap	African	Sub	692	C=0.798	T=0.202
HapMap	Asian	Sub	254	C=0.693	T=0.307
HapMap	Europe	Sub	172	C=0.738	T=0.262
Genome-wide autozygosity in Daghestan	Global	Study-wide	1132	C=0.7571	T=0.2429
Genome-wide autozygosity in Daghestan	Daghestan	Sub	624	C=0.752	T=0.248
Genome-wide autozygosity in Daghestan	Near_East	Sub	144	C=0.792	T=0.208
Genome-wide autozygosity in Daghestan	Central Asia	Sub	122	C=0.779	T=0.221
Genome-wide autozygosity in Daghestan	Europe	Sub	108	C=0.731	T=0.269
Genome-wide autozygosity in Daghestan	South Asian	Sub	98	C=0.76	T=0.24
Genome-wide autozygosity in Daghestan	Caucasus	Sub	36	C=0.72	T=0.28
Genome of the Netherlands Release 5	Genome of the Netherlands	Study-wide	998	C=0.760	T=0.240
Chileans	Chilean	Study-wide	626	C=0.853	T=0.147
Northern Sweden	ACPOP	Study-wide	600	C=0.828	T=0.172
SGDP_PRJ	Global	Study-wide	252	C=0.468	T=0.532
Qatari	Global	Study-wide	216	C=0.708	T=0.292
A Vietnamese Genetic Variation Database	Global	Study-wide	216	C=0.694	T=0.306
Ancient Sardinia genome-wide 1240k capture data generation and analysis	Global	Study-wide	80	C=0.68	T=0.33
The Danish reference pan genome	Danish	Study-wide	40	C=0.90	T=0.10
Siberian	Global	Study-wide	20	C=0.45	T=0.55

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 8	NC_000008.11:g.41615326C>G
GRCh38.p14 chr 8	NC_000008.11:g.41615326C>T
GRCh37.p13 chr 8	NC_000008.10:g.41472845C>G
GRCh37.p13 chr 8	NC_000008.10:g.41472845C>T

Gene: GPAT4, glycerol-3-phosphate acyltransferase 4 (plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
GPAT4 transcript variant 2	NM_001363197.2:c.1053+278… NM_001363197.2:c.1053+278C>G	N/A	Intron Variant
GPAT4 transcript variant 3	NM_001363198.2:c.429+278C… NM_001363198.2:c.429+278C>G	N/A	Intron Variant
GPAT4 transcript variant 1	NM_178819.4:c.1053+278C>G	N/A	Intron Variant
GPAT4 transcript variant X1	XM_047421370.1:c.1053+278… XM_047421370.1:c.1053+278C>G	N/A	Intron Variant
GPAT4 transcript variant X2	XM_047421371.1:c.1053+278… XM_047421371.1:c.1053+278C>G	N/A	Intron Variant
GPAT4 transcript variant X3	XM_047421372.1:c.1053+278… XM_047421372.1:c.1053+278C>G	N/A	Intron Variant
GPAT4 transcript variant X4	XM_047421374.1:c.429+278C… XM_047421374.1:c.429+278C>G	N/A	Intron 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=	G	T
GRCh38.p14 chr 8	NC_000008.11:g.41615326=	NC_000008.11:g.41615326C>G	NC_000008.11:g.41615326C>T
GRCh37.p13 chr 8	NC_000008.10:g.41472845=	NC_000008.10:g.41472845C>G	NC_000008.10:g.41472845C>T
GPAT4 transcript variant 2	NM_001363197.2:c.1053+278=	NM_001363197.2:c.1053+278C>G	NM_001363197.2:c.1053+278C>T
GPAT4 transcript variant 3	NM_001363198.2:c.429+278=	NM_001363198.2:c.429+278C>G	NM_001363198.2:c.429+278C>T
GPAT4 transcript variant 1	NM_178819.3:c.1053+278=	NM_178819.3:c.1053+278C>G	NM_178819.3:c.1053+278C>T
GPAT4 transcript variant 1	NM_178819.4:c.1053+278=	NM_178819.4:c.1053+278C>G	NM_178819.4:c.1053+278C>T
AGPAT6 transcript variant X1	XM_005273402.1:c.1053+278=	XM_005273402.1:c.1053+278C>G	XM_005273402.1:c.1053+278C>T
AGPAT6 transcript variant X2	XM_005273403.1:c.429+278=	XM_005273403.1:c.429+278C>G	XM_005273403.1:c.429+278C>T
GPAT4 transcript variant X1	XM_047421370.1:c.1053+278=	XM_047421370.1:c.1053+278C>G	XM_047421370.1:c.1053+278C>T
GPAT4 transcript variant X2	XM_047421371.1:c.1053+278=	XM_047421371.1:c.1053+278C>G	XM_047421371.1:c.1053+278C>T
GPAT4 transcript variant X3	XM_047421372.1:c.1053+278=	XM_047421372.1:c.1053+278C>G	XM_047421372.1:c.1053+278C>T
GPAT4 transcript variant X4	XM_047421374.1:c.429+278=	XM_047421374.1:c.429+278C>G	XM_047421374.1:c.429+278C>T

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#.

68 SubSNP, 22 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	CSHL-HAPMAP	ss20338803	Feb 28, 2004 (120)
2	PERLEGEN	ss24476357	Sep 20, 2004 (123)
3	ABI	ss44850029	Mar 14, 2006 (126)
4	AFFY	ss76563158	Dec 06, 2007 (129)
5	HGSV	ss82760326	Dec 15, 2007 (130)
6	HUMANGENOME_JCVI	ss98068853	Feb 06, 2009 (130)
7	KRIBB_YJKIM	ss105063967	Feb 06, 2009 (130)
8	ENSEMBL	ss134405698	Dec 01, 2009 (131)
9	BUSHMAN	ss199083434	Jul 04, 2010 (132)
10	BCM-HGSC-SUB	ss208547781	Jul 04, 2010 (132)
11	1000GENOMES	ss223671461	Jul 14, 2010 (132)
12	1000GENOMES	ss234413551	Jul 15, 2010 (132)
13	1000GENOMES	ss241275065	Jul 15, 2010 (132)
14	GMI	ss279783474	May 04, 2012 (137)
15	GMI	ss285834240	Apr 25, 2013 (138)
16	PJP	ss294263540	May 09, 2011 (134)
17	TISHKOFF	ss560706996	Apr 25, 2013 (138)
18	SSMP	ss655139364	Apr 25, 2013 (138)
19	EVA-GONL	ss985439452	Aug 21, 2014 (142)
20	JMKIDD_LAB	ss1075466159	Aug 21, 2014 (142)
21	1000GENOMES	ss1329553827	Aug 21, 2014 (142)
22	HAMMER_LAB	ss1397524549	Sep 08, 2015 (146)
23	DDI	ss1431491905	Apr 01, 2015 (144)
24	EVA_GENOME_DK	ss1582658576	Apr 01, 2015 (144)
25	EVA_DECODE	ss1595036547	Apr 01, 2015 (144)
26	EVA_UK10K_ALSPAC	ss1620477595	Apr 01, 2015 (144)
27	EVA_UK10K_TWINSUK	ss1663471628	Apr 01, 2015 (144)
28	EVA_SVP	ss1713032626	Apr 01, 2015 (144)
29	HAMMER_LAB	ss1805505313	Sep 08, 2015 (146)
30	WEILL_CORNELL_DGM	ss1928728748	Feb 12, 2016 (147)
31	JJLAB	ss2025067496	Sep 14, 2016 (149)
32	USC_VALOUEV	ss2153289683	Dec 20, 2016 (150)
33	HUMAN_LONGEVITY	ss2302630501	Dec 20, 2016 (150)
34	SYSTEMSBIOZJU	ss2627016180	Nov 08, 2017 (151)
35	GRF	ss2709055647	Nov 08, 2017 (151)
36	GNOMAD	ss2865897852	Nov 08, 2017 (151)
37	SWEGEN	ss3003056149	Nov 08, 2017 (151)
38	BIOINF_KMB_FNS_UNIBA	ss3026324060	Nov 08, 2017 (151)
39	CSHL	ss3348151713	Nov 08, 2017 (151)
40	URBANLAB	ss3648902034	Oct 12, 2018 (152)
41	EGCUT_WGS	ss3670750149	Jul 13, 2019 (153)
42	EVA_DECODE	ss3721875838	Jul 13, 2019 (153)
43	ACPOP	ss3735604712	Jul 13, 2019 (153)
44	EVA	ss3767913307	Jul 13, 2019 (153)
45	PACBIO	ss3786128728	Jul 13, 2019 (153)
46	PACBIO	ss3791388314	Jul 13, 2019 (153)
47	PACBIO	ss3796269602	Jul 13, 2019 (153)
48	KHV_HUMAN_GENOMES	ss3811073951	Jul 13, 2019 (153)
49	EVA	ss3831134383	Apr 26, 2020 (154)
50	EVA	ss3839077455	Apr 26, 2020 (154)
51	EVA	ss3844536279	Apr 26, 2020 (154)
52	SGDP_PRJ	ss3869772169	Apr 26, 2020 (154)
53	KRGDB	ss3917227856	Apr 26, 2020 (154)
54	EVA	ss3985356985	Apr 26, 2021 (155)
55	TOPMED	ss4783531003	Apr 26, 2021 (155)
56	TOMMO_GENOMICS	ss5188367274	Apr 26, 2021 (155)
57	1000G_HIGH_COVERAGE	ss5276885480	Oct 17, 2022 (156)
58	EVA	ss5380676497	Oct 17, 2022 (156)
59	HUGCELL_USP	ss5473487313	Oct 17, 2022 (156)
60	EVA	ss5509327622	Oct 17, 2022 (156)
61	1000G_HIGH_COVERAGE	ss5567094689	Oct 17, 2022 (156)
62	SANFORD_IMAGENETICS	ss5645238327	Oct 17, 2022 (156)
63	TOMMO_GENOMICS	ss5730191828	Oct 17, 2022 (156)
64	YY_MCH	ss5809647458	Oct 17, 2022 (156)
65	EVA	ss5830437215	Oct 17, 2022 (156)
66	EVA	ss5856350798	Oct 17, 2022 (156)
67	EVA	ss5888670042	Oct 17, 2022 (156)
68	EVA	ss5974437939	Oct 17, 2022 (156)
69	1000Genomes	NC_000008.10 - 41472845	Oct 12, 2018 (152)
70	1000Genomes_30x	NC_000008.11 - 41615326	Oct 17, 2022 (156)
71	The Avon Longitudinal Study of Parents and Children	NC_000008.10 - 41472845	Oct 12, 2018 (152)
72	Chileans	NC_000008.10 - 41472845	Apr 26, 2020 (154)
73	Genome-wide autozygosity in Daghestan	NC_000008.9 - 41592002	Apr 26, 2020 (154)
74	Genetic variation in the Estonian population	NC_000008.10 - 41472845	Oct 12, 2018 (152)
75	The Danish reference pan genome	NC_000008.10 - 41472845	Apr 26, 2020 (154)
76	gnomAD - Genomes	NC_000008.11 - 41615326	Apr 26, 2021 (155)
77	Genome of the Netherlands Release 5	NC_000008.10 - 41472845	Apr 26, 2020 (154)
78	HapMap	NC_000008.11 - 41615326	Apr 26, 2020 (154)
79	KOREAN population from KRGDB	NC_000008.10 - 41472845	Apr 26, 2020 (154)
80	Northern Sweden	NC_000008.10 - 41472845	Jul 13, 2019 (153)
81	Ancient Sardinia genome-wide 1240k capture data generation and analysis	NC_000008.10 - 41472845	Apr 26, 2021 (155)
82	Qatari	NC_000008.10 - 41472845	Apr 26, 2020 (154)
83	SGDP_PRJ	NC_000008.10 - 41472845	Apr 26, 2020 (154)
84	Siberian	NC_000008.10 - 41472845	Apr 26, 2020 (154)
85	8.3KJPN	NC_000008.10 - 41472845	Apr 26, 2021 (155)
86	14KJPN	NC_000008.11 - 41615326	Oct 17, 2022 (156)
87	TopMed	NC_000008.11 - 41615326	Apr 26, 2021 (155)
88	UK 10K study - Twins	NC_000008.10 - 41472845	Oct 12, 2018 (152)
89	A Vietnamese Genetic Variation Database	NC_000008.10 - 41472845	Jul 13, 2019 (153)
90	ALFA	NC_000008.11 - 41615326	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).

Associated ID	History Updated (Build)
rs17658782	Oct 07, 2004 (123)
rs60206493	May 25, 2008 (130)

Added to this RefSNP Cluster:

Submission IDs	Observation SPDI	Canonical SPDI	Source RSIDs
24405250, ss3917227856	NC_000008.10:41472844:C:G	NC_000008.11:41615325:C:G	(self)
498398, ss82760326, ss199083434, ss208547781, ss279783474, ss285834240, ss294263540, ss1397524549, ss1595036547, ss1713032626	NC_000008.9:41592001:C:T	NC_000008.11:41615325:C:T	(self)
41669694, 23173555, 433716, 16488397, 8823514, 10349536, 24405250, 8889577, 582912, 10770678, 21789149, 5806037, 46336581, 23173555, 5162689, ss223671461, ss234413551, ss241275065, ss560706996, ss655139364, ss985439452, ss1075466159, ss1329553827, ss1431491905, ss1582658576, ss1620477595, ss1663471628, ss1805505313, ss1928728748, ss2025067496, ss2153289683, ss2627016180, ss2709055647, ss2865897852, ss3003056149, ss3348151713, ss3670750149, ss3735604712, ss3767913307, ss3786128728, ss3791388314, ss3796269602, ss3831134383, ss3839077455, ss3869772169, ss3917227856, ss3985356985, ss5188367274, ss5380676497, ss5509327622, ss5645238327, ss5830437215, ss5974437939	NC_000008.10:41472844:C:T	NC_000008.11:41615325:C:T	(self)
54620624, 293812267, 3612560, 64028932, 620908563, 5225936221, ss2302630501, ss3026324060, ss3648902034, ss3721875838, ss3811073951, ss3844536279, ss4783531003, ss5276885480, ss5473487313, ss5567094689, ss5730191828, ss5809647458, ss5856350798, ss5888670042	NC_000008.11:41615325:C:T	NC_000008.11:41615325:C:T	(self)
ss20338803	NT_008251.14:3535109:C:T	NC_000008.11:41615325:C:T	(self)
ss24476357, ss44850029, ss76563158, ss98068853, ss105063967, ss134405698	NT_167187.1:29330990:C:T	NC_000008.11:41615325:C:T	(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 rs12677439

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.

Choose placement

dbSNP Short Genetic Variations

Welcome to the Reference SNP (rs) Report

Reference SNP (rs) Report

rs12677439