Name: rs79434847
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.

rs79434847

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr2:134872337 (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: T>A / T>C
Variation Type: SNV Single Nucleotide Variation
Frequency: C=0.021712 (5747/264690, TOPMED)
C=0.016188 (2270/140224, GnomAD)
C=0.27046 (7642/28256, 14KJPN) (+ 15 more)
C=0.26951 (4517/16760, 8.3KJPN)
C=0.01617 (270/16702, ALFA)
C=0.0710 (455/6404, 1000G_30x)
C=0.0749 (375/5008, 1000G)
C=0.0266 (119/4480, Estonian)
C=0.0036 (14/3854, ALSPAC)
C=0.0027 (10/3708, TWINSUK)
C=0.2785 (816/2930, KOREAN)
C=0.2778 (509/1832, Korea1K)
C=0.004 (2/534, MGP)
C=0.019 (4/216, Qatari)
C=0.349 (74/212, Vietnamese)
T=0.43 (40/92, SGDP_PRJ)
T=0.5 (4/8, Siberian)
C=0.5 (4/8, Siberian)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: ACMSD : Intron Variant
CCNT2-AS1 : 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	16702	T=0.98383	C=0.01617
European	Sub	12214	T=0.98706	C=0.01294
African	Sub	2864	T=0.9867	C=0.0133
African Others	Sub	108	T=1.000	C=0.000
African American	Sub	2756	T=0.9862	C=0.0138
Asian	Sub	108	T=0.759	C=0.241
East Asian	Sub	84	T=0.76	C=0.24
Other Asian	Sub	24	T=0.75	C=0.25
Latin American 1	Sub	146	T=0.986	C=0.014
Latin American 2	Sub	610	T=0.956	C=0.044
South Asian	Sub	94	T=0.98	C=0.02
Other	Sub	666	T=0.974	C=0.026

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	T=0.978288	C=0.021712
gnomAD - Genomes	Global	Study-wide	140224	T=0.983812	C=0.016188
gnomAD - Genomes	European	Sub	75942	T=0.99352	C=0.00648
gnomAD - Genomes	African	Sub	42020	T=0.98693	C=0.01307
gnomAD - Genomes	American	Sub	13658	T=0.98206	C=0.01794
gnomAD - Genomes	Ashkenazi Jewish	Sub	3324	T=0.9970	C=0.0030
gnomAD - Genomes	East Asian	Sub	3128	T=0.7052	C=0.2948
gnomAD - Genomes	Other	Sub	2152	T=0.9758	C=0.0242
14KJPN	JAPANESE	Study-wide	28256	T=0.72954	C=0.27046
8.3KJPN	JAPANESE	Study-wide	16760	T=0.73049	C=0.26951
Allele Frequency Aggregator	Total	Global	16702	T=0.98383	C=0.01617
Allele Frequency Aggregator	European	Sub	12214	T=0.98706	C=0.01294
Allele Frequency Aggregator	African	Sub	2864	T=0.9867	C=0.0133
Allele Frequency Aggregator	Other	Sub	666	T=0.974	C=0.026
Allele Frequency Aggregator	Latin American 2	Sub	610	T=0.956	C=0.044
Allele Frequency Aggregator	Latin American 1	Sub	146	T=0.986	C=0.014
Allele Frequency Aggregator	Asian	Sub	108	T=0.759	C=0.241
Allele Frequency Aggregator	South Asian	Sub	94	T=0.98	C=0.02
1000Genomes_30x	Global	Study-wide	6404	T=0.9290	C=0.0710
1000Genomes_30x	African	Sub	1786	T=0.9787	C=0.0213
1000Genomes_30x	Europe	Sub	1266	T=0.9945	C=0.0055
1000Genomes_30x	South Asian	Sub	1202	T=0.9700	C=0.0300
1000Genomes_30x	East Asian	Sub	1170	T=0.7051	C=0.2949
1000Genomes_30x	American	Sub	980	T=0.970	C=0.030
1000Genomes	Global	Study-wide	5008	T=0.9251	C=0.0749
1000Genomes	African	Sub	1322	T=0.9788	C=0.0212
1000Genomes	East Asian	Sub	1008	T=0.7083	C=0.2917
1000Genomes	Europe	Sub	1006	T=0.9930	C=0.0070
1000Genomes	South Asian	Sub	978	T=0.971	C=0.029
1000Genomes	American	Sub	694	T=0.974	C=0.026
Genetic variation in the Estonian population	Estonian	Study-wide	4480	T=0.9734	C=0.0266
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	T=0.9964	C=0.0036
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	T=0.9973	C=0.0027
KOREAN population from KRGDB	KOREAN	Study-wide	2930	T=0.7215	A=0.0000, C=0.2785
Korean Genome Project	KOREAN	Study-wide	1832	T=0.7222	C=0.2778
Medical Genome Project healthy controls from Spanish population	Spanish controls	Study-wide	534	T=0.996	C=0.004
Qatari	Global	Study-wide	216	T=0.981	C=0.019
A Vietnamese Genetic Variation Database	Global	Study-wide	212	T=0.651	C=0.349
SGDP_PRJ	Global	Study-wide	92	T=0.43	C=0.57
Siberian	Global	Study-wide	8	T=0.5	C=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 2	NC_000002.12:g.134872337T>A
GRCh38.p14 chr 2	NC_000002.12:g.134872337T>C
GRCh37.p13 chr 2	NC_000002.11:g.135629907T>A
GRCh37.p13 chr 2	NC_000002.11:g.135629907T>C

Gene: ACMSD, aminocarboxymuconate semialdehyde decarboxylase (plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
ACMSD transcript variant 2	NM_001307983.2:c.503-132T… NM_001307983.2:c.503-132T>A	N/A	Intron Variant
ACMSD transcript variant 1	NM_138326.3:c.677-132T>A	N/A	Intron Variant
ACMSD transcript variant X1	XM_005263586.5:c.530-132T… XM_005263586.5:c.530-132T>A	N/A	Intron Variant
ACMSD transcript variant X5	XM_005263588.5:c.503-132T… XM_005263588.5:c.503-132T>A	N/A	Intron Variant
ACMSD transcript variant X6	XM_005263590.5:c.470-132T… XM_005263590.5:c.470-132T>A	N/A	Intron Variant
ACMSD transcript variant X2	XM_011510592.3:c.503-132T… XM_011510592.3:c.503-132T>A	N/A	Intron Variant
ACMSD transcript variant X3	XM_017003325.2:c.503-132T… XM_017003325.2:c.503-132T>A	N/A	Intron Variant
ACMSD transcript variant X4	XM_017003326.2:c.503-132T… XM_017003326.2:c.503-132T>A	N/A	Intron Variant
ACMSD transcript variant X7	XM_047443333.1:c.323-132T… XM_047443333.1:c.323-132T>A	N/A	Intron Variant

Gene: CCNT2-AS1, CCNT2 antisense RNA 1 (minus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
CCNT2-AS1 transcript	NR_036549.1:n.	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	T=	A	C
GRCh38.p14 chr 2	NC_000002.12:g.134872337=	NC_000002.12:g.134872337T>A	NC_000002.12:g.134872337T>C
GRCh37.p13 chr 2	NC_000002.11:g.135629907=	NC_000002.11:g.135629907T>A	NC_000002.11:g.135629907T>C
ACMSD transcript variant 2	NM_001307983.2:c.503-132=	NM_001307983.2:c.503-132T>A	NM_001307983.2:c.503-132T>C
ACMSD transcript variant 1	NM_138326.2:c.677-132=	NM_138326.2:c.677-132T>A	NM_138326.2:c.677-132T>C
ACMSD transcript variant 1	NM_138326.3:c.677-132=	NM_138326.3:c.677-132T>A	NM_138326.3:c.677-132T>C
ACMSD transcript variant X1	XM_005263586.1:c.530-132=	XM_005263586.1:c.530-132T>A	XM_005263586.1:c.530-132T>C
ACMSD transcript variant X1	XM_005263586.5:c.530-132=	XM_005263586.5:c.530-132T>A	XM_005263586.5:c.530-132T>C
ACMSD transcript variant X2	XM_005263587.1:c.503-132=	XM_005263587.1:c.503-132T>A	XM_005263587.1:c.503-132T>C
ACMSD transcript variant X3	XM_005263588.1:c.503-132=	XM_005263588.1:c.503-132T>A	XM_005263588.1:c.503-132T>C
ACMSD transcript variant X5	XM_005263588.5:c.503-132=	XM_005263588.5:c.503-132T>A	XM_005263588.5:c.503-132T>C
ACMSD transcript variant X4	XM_005263589.1:c.491-132=	XM_005263589.1:c.491-132T>A	XM_005263589.1:c.491-132T>C
ACMSD transcript variant X5	XM_005263590.1:c.470-132=	XM_005263590.1:c.470-132T>A	XM_005263590.1:c.470-132T>C
ACMSD transcript variant X6	XM_005263590.5:c.470-132=	XM_005263590.5:c.470-132T>A	XM_005263590.5:c.470-132T>C
ACMSD transcript variant X2	XM_011510592.3:c.503-132=	XM_011510592.3:c.503-132T>A	XM_011510592.3:c.503-132T>C
ACMSD transcript variant X3	XM_017003325.2:c.503-132=	XM_017003325.2:c.503-132T>A	XM_017003325.2:c.503-132T>C
ACMSD transcript variant X4	XM_017003326.2:c.503-132=	XM_017003326.2:c.503-132T>A	XM_017003326.2:c.503-132T>C
ACMSD transcript variant X7	XM_047443333.1:c.323-132=	XM_047443333.1:c.323-132T>A	XM_047443333.1:c.323-132T>C

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#.

39 SubSNP, 17 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	GMI	ss157714884	Dec 01, 2009 (131)
2	1000GENOMES	ss238878948	Jul 15, 2010 (132)
3	GMI	ss276691749	May 04, 2012 (137)
4	SSMP	ss649521005	Apr 25, 2013 (138)
5	JMKIDD_LAB	ss1069516344	Aug 21, 2014 (142)
6	1000GENOMES	ss1299435957	Aug 21, 2014 (142)
7	EVA_UK10K_ALSPAC	ss1604621235	Apr 01, 2015 (144)
8	EVA_UK10K_TWINSUK	ss1647615268	Apr 01, 2015 (144)
9	EVA_MGP	ss1710981387	Apr 01, 2015 (144)
10	WEILL_CORNELL_DGM	ss1920644387	Feb 12, 2016 (147)
11	USC_VALOUEV	ss2148912115	Dec 20, 2016 (150)
12	HUMAN_LONGEVITY	ss2234496083	Dec 20, 2016 (150)
13	SYSTEMSBIOZJU	ss2624929783	Nov 08, 2017 (151)
14	GRF	ss2703536535	Nov 08, 2017 (151)
15	GNOMAD	ss2779968996	Nov 08, 2017 (151)
16	SWEGEN	ss2990472915	Nov 08, 2017 (151)
17	EGCUT_WGS	ss3658314948	Jul 13, 2019 (153)
18	EVA_DECODE	ss3704944602	Jul 13, 2019 (153)
19	EVA	ss3757414987	Jul 13, 2019 (153)
20	KHV_HUMAN_GENOMES	ss3801782462	Jul 13, 2019 (153)
21	SGDP_PRJ	ss3853471741	Apr 25, 2020 (154)
22	KRGDB	ss3899031859	Apr 25, 2020 (154)
23	KOGIC	ss3949022418	Apr 25, 2020 (154)
24	EVA	ss3986198004	Apr 26, 2021 (155)
25	TOPMED	ss4524862982	Apr 26, 2021 (155)
26	TOMMO_GENOMICS	ss5153989187	Apr 26, 2021 (155)
27	1000G_HIGH_COVERAGE	ss5250110205	Oct 12, 2022 (156)
28	EVA	ss5332513433	Oct 12, 2022 (156)
29	HUGCELL_USP	ss5449913394	Oct 12, 2022 (156)
30	EVA	ss5506598116	Oct 12, 2022 (156)
31	1000G_HIGH_COVERAGE	ss5526427438	Oct 12, 2022 (156)
32	SANFORD_IMAGENETICS	ss5629862975	Oct 12, 2022 (156)
33	TOMMO_GENOMICS	ss5684151144	Oct 12, 2022 (156)
34	YY_MCH	ss5802747498	Oct 12, 2022 (156)
35	EVA	ss5820842933	Oct 12, 2022 (156)
36	EVA	ss5848523990	Oct 12, 2022 (156)
37	EVA	ss5852725422	Oct 12, 2022 (156)
38	EVA	ss5932479464	Oct 12, 2022 (156)
39	EVA	ss5956064990	Oct 12, 2022 (156)
40	1000Genomes	NC_000002.11 - 135629907	Oct 11, 2018 (152)
41	1000Genomes_30x	NC_000002.12 - 134872337	Oct 12, 2022 (156)
42	The Avon Longitudinal Study of Parents and Children	NC_000002.11 - 135629907	Oct 11, 2018 (152)
43	Genetic variation in the Estonian population	NC_000002.11 - 135629907	Oct 11, 2018 (152)
44	gnomAD - Genomes	NC_000002.12 - 134872337	Apr 26, 2021 (155)
45	KOREAN population from KRGDB	NC_000002.11 - 135629907	Apr 25, 2020 (154)
46	Korean Genome Project	NC_000002.12 - 134872337	Apr 25, 2020 (154)
47	Medical Genome Project healthy controls from Spanish population	NC_000002.11 - 135629907	Apr 25, 2020 (154)
48	Qatari	NC_000002.11 - 135629907	Apr 25, 2020 (154)
49	SGDP_PRJ	NC_000002.11 - 135629907	Apr 25, 2020 (154)
50	Siberian	NC_000002.11 - 135629907	Apr 25, 2020 (154)
51	8.3KJPN	NC_000002.11 - 135629907	Apr 26, 2021 (155)
52	14KJPN	NC_000002.12 - 134872337	Oct 12, 2022 (156)
53	TopMed	NC_000002.12 - 134872337	Apr 26, 2021 (155)
54	UK 10K study - Twins	NC_000002.11 - 135629907	Oct 11, 2018 (152)
55	A Vietnamese Genetic Variation Database	NC_000002.11 - 135629907	Jul 13, 2019 (153)
56	ALFA	NC_000002.12 - 134872337	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
6209253, ss3899031859	NC_000002.11:135629906:T:A	NC_000002.12:134872336:T:A	(self)
ss276691749	NC_000002.10:135346376:T:C	NC_000002.12:134872336:T:C	(self)
10455619, 5758883, 4053196, 6209253, 97926, 2686317, 5488721, 1428469, 11958494, 5758883, 1246242, ss238878948, ss649521005, ss1069516344, ss1299435957, ss1604621235, ss1647615268, ss1710981387, ss1920644387, ss2148912115, ss2624929783, ss2703536535, ss2779968996, ss2990472915, ss3658314948, ss3757414987, ss3853471741, ss3899031859, ss3986198004, ss5153989187, ss5332513433, ss5506598116, ss5629862975, ss5820842933, ss5848523990, ss5956064990	NC_000002.11:135629906:T:C	NC_000002.12:134872336:T:C	(self)
13953373, 74539476, 5400419, 17988248, 328685861, 1738048606, ss2234496083, ss3704944602, ss3801782462, ss3949022418, ss4524862982, ss5250110205, ss5449913394, ss5526427438, ss5684151144, ss5802747498, ss5852725422, ss5932479464	NC_000002.12:134872336:T:C	NC_000002.12:134872336:T:C	(self)
ss157714884	NT_022135.16:25378569:T:C	NC_000002.12:134872336:T:C	(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 rs79434847

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
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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

rs79434847