Name: rs13423840
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.

rs13423840

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr2:165764903 (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>T
Variation Type: SNV Single Nucleotide Variation
Frequency: T=0.008591 (2274/264690, TOPMED)
T=0.002103 (528/251106, GnomAD_exome)
T=0.008016 (1124/140224, GnomAD) (+ 10 more)
T=0.002793 (339/121394, ExAC)
T=0.01166 (918/78702, PAGE_STUDY)
T=0.00246 (142/57772, ALFA)
T=0.00976 (127/13006, GO-ESP)
T=0.0108 (69/6404, 1000G_30x)
T=0.0100 (50/5008, 1000G)
T=0.031 (31/998, HapMap)
T=0.014 (3/216, Qatari)
C=0.5 (4/8, SGDP_PRJ)
T=0.5 (4/8, SGDP_PRJ)

Clinical Significance: Reported in ClinVar
Gene : Consequence: GALNT3 : Synonymous 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	74134	C=0.99610	T=0.00390
European	Sub	53294	C=0.99981	T=0.00019
African	Sub	10152	C=0.97449	T=0.02551
African Others	Sub	346	C=0.988	T=0.012
African American	Sub	9806	C=0.9740	T=0.0260
Asian	Sub	216	C=1.000	T=0.000
East Asian	Sub	158	C=1.000	T=0.000
Other Asian	Sub	58	C=1.00	T=0.00
Latin American 1	Sub	518	C=0.992	T=0.008
Latin American 2	Sub	702	C=1.000	T=0.000
South Asian	Sub	120	C=1.000	T=0.000
Other	Sub	9132	C=0.9982	T=0.0018

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=0.991409	T=0.008591
gnomAD - Exomes	Global	Study-wide	251106	C=0.997897	T=0.002103
gnomAD - Exomes	European	Sub	135058	C=0.999904	T=0.000096
gnomAD - Exomes	Asian	Sub	49008	C=0.99998	T=0.00002
gnomAD - Exomes	American	Sub	34590	C=0.99893	T=0.00107
gnomAD - Exomes	African	Sub	16256	C=0.97115	T=0.02885
gnomAD - Exomes	Ashkenazi Jewish	Sub	10070	C=1.00000	T=0.00000
gnomAD - Exomes	Other	Sub	6124	C=0.9987	T=0.0013
gnomAD - Genomes	Global	Study-wide	140224	C=0.991984	T=0.008016
gnomAD - Genomes	European	Sub	75938	C=0.99979	T=0.00021
gnomAD - Genomes	African	Sub	42030	C=0.97526	T=0.02474
gnomAD - Genomes	American	Sub	13654	C=0.99663	T=0.00337
gnomAD - Genomes	Ashkenazi Jewish	Sub	3320	C=1.0000	T=0.0000
gnomAD - Genomes	East Asian	Sub	3132	C=1.0000	T=0.0000
gnomAD - Genomes	Other	Sub	2150	C=0.9898	T=0.0102
ExAC	Global	Study-wide	121394	C=0.997207	T=0.002793
ExAC	Europe	Sub	73344	C=0.99990	T=0.00010
ExAC	Asian	Sub	25164	C=0.99996	T=0.00004
ExAC	American	Sub	11578	C=0.99940	T=0.00060
ExAC	African	Sub	10400	C=0.96904	T=0.03096
ExAC	Other	Sub	908	C=0.998	T=0.002
The PAGE Study	Global	Study-wide	78702	C=0.98834	T=0.01166
The PAGE Study	AfricanAmerican	Sub	32516	C=0.97604	T=0.02396
The PAGE Study	Mexican	Sub	10810	C=0.99917	T=0.00083
The PAGE Study	Asian	Sub	8318	C=1.0000	T=0.0000
The PAGE Study	PuertoRican	Sub	7918	C=0.9901	T=0.0099
The PAGE Study	NativeHawaiian	Sub	4534	C=0.9998	T=0.0002
The PAGE Study	Cuban	Sub	4230	C=0.9979	T=0.0021
The PAGE Study	Dominican	Sub	3828	C=0.9916	T=0.0084
The PAGE Study	CentralAmerican	Sub	2450	C=0.9976	T=0.0024
The PAGE Study	SouthAmerican	Sub	1982	C=0.9990	T=0.0010
The PAGE Study	NativeAmerican	Sub	1260	C=0.9984	T=0.0016
The PAGE Study	SouthAsian	Sub	856	C=1.000	T=0.000
Allele Frequency Aggregator	Total	Global	57772	C=0.99754	T=0.00246
Allele Frequency Aggregator	European	Sub	43204	C=0.99979	T=0.00021
Allele Frequency Aggregator	Other	Sub	7698	C=0.9984	T=0.0016
Allele Frequency Aggregator	African	Sub	5314	C=0.9780	T=0.0220
Allele Frequency Aggregator	Latin American 2	Sub	702	C=1.000	T=0.000
Allele Frequency Aggregator	Latin American 1	Sub	518	C=0.992	T=0.008
Allele Frequency Aggregator	Asian	Sub	216	C=1.000	T=0.000
Allele Frequency Aggregator	South Asian	Sub	120	C=1.000	T=0.000
GO Exome Sequencing Project	Global	Study-wide	13006	C=0.99024	T=0.00976
GO Exome Sequencing Project	European American	Sub	8600	C=0.9999	T=0.0001
GO Exome Sequencing Project	African American	Sub	4406	C=0.9714	T=0.0286
1000Genomes_30x	Global	Study-wide	6404	C=0.9892	T=0.0108
1000Genomes_30x	African	Sub	1786	C=0.9653	T=0.0347
1000Genomes_30x	Europe	Sub	1266	C=1.0000	T=0.0000
1000Genomes_30x	South Asian	Sub	1202	C=1.0000	T=0.0000
1000Genomes_30x	East Asian	Sub	1170	C=1.0000	T=0.0000
1000Genomes_30x	American	Sub	980	C=0.993	T=0.007
1000Genomes	Global	Study-wide	5008	C=0.9900	T=0.0100
1000Genomes	African	Sub	1322	C=0.9660	T=0.0340
1000Genomes	East Asian	Sub	1008	C=1.0000	T=0.0000
1000Genomes	Europe	Sub	1006	C=1.0000	T=0.0000
1000Genomes	South Asian	Sub	978	C=1.000	T=0.000
1000Genomes	American	Sub	694	C=0.993	T=0.007
HapMap	Global	Study-wide	998	C=0.969	T=0.031
HapMap	African	Sub	692	C=0.961	T=0.039
HapMap	American	Sub	218	C=0.982	T=0.018
HapMap	Asian	Sub	88	C=1.00	T=0.00
Qatari	Global	Study-wide	216	C=0.986	T=0.014
SGDP_PRJ	Global	Study-wide	8	C=0.5	T=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.165764903C>T
GRCh37.p13 chr 2	NC_000002.11:g.166621413C>T
GALNT3 RefSeqGene	NG_012069.1:g.34391G>A

Gene: GALNT3, polypeptide N-acetylgalactosaminyltransferase 3 (minus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
GALNT3 transcript	NM_004482.4:c.669G>A	V [GTG] > V [GTA]	Coding Sequence Variant
polypeptide N-acetylgalactosaminyltransferase 3	NP_004473.2:p.Val223=	V (Val) > V (Val)	Synonymous Variant
GALNT3 transcript variant X1	XM_005246449.2:c.669G>A	V [GTG] > V [GTA]	Coding Sequence Variant
polypeptide N-acetylgalactosaminyltransferase 3 isoform X1	XP_005246506.1:p.Val223=	V (Val) > V (Val)	Synonymous Variant
GALNT3 transcript variant X2	XM_017003770.2:c.669G>A	V [GTG] > V [GTA]	Coding Sequence Variant
polypeptide N-acetylgalactosaminyltransferase 3 isoform X1	XP_016859259.1:p.Val223=	V (Val) > V (Val)	Synonymous Variant
GALNT3 transcript variant X3	XM_011510929.2:c.669G>A	V [GTG] > V [GTA]	Coding Sequence Variant
polypeptide N-acetylgalactosaminyltransferase 3 isoform X1	XP_011509231.1:p.Val223=	V (Val) > V (Val)	Synonymous Variant
GALNT3 transcript variant X4	XM_047443883.1:c.669G>A	V [GTG] > V [GTA]	Coding Sequence Variant
polypeptide N-acetylgalactosaminyltransferase 3 isoform X2	XP_047299839.1:p.Val223=	V (Val) > V (Val)	Synonymous 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.

Allele: T (allele ID: 284700 )

ClinVar Accession	Disease Names	Clinical Significance
RCV000361417.3	Tumoral calcinosis, hyperphosphatemic, familial, 1	Benign
RCV000958588.6	not provided	Benign

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=	T
GRCh38.p14 chr 2	NC_000002.12:g.165764903=	NC_000002.12:g.165764903C>T
GRCh37.p13 chr 2	NC_000002.11:g.166621413=	NC_000002.11:g.166621413C>T
GALNT3 RefSeqGene	NG_012069.1:g.34391=	NG_012069.1:g.34391G>A
GALNT3 transcript	NM_004482.4:c.669=	NM_004482.4:c.669G>A
GALNT3 transcript	NM_004482.3:c.669=	NM_004482.3:c.669G>A
GALNT3 transcript variant X1	XM_005246449.2:c.669=	XM_005246449.2:c.669G>A
GALNT3 transcript variant X3	XM_005246449.1:c.669=	XM_005246449.1:c.669G>A
GALNT3 transcript variant X2	XM_017003770.2:c.669=	XM_017003770.2:c.669G>A
GALNT3 transcript variant X1	XM_017003770.1:c.669=	XM_017003770.1:c.669G>A
GALNT3 transcript variant X3	XM_011510929.2:c.669=	XM_011510929.2:c.669G>A
GALNT3 transcript variant X2	XM_011510929.1:c.669=	XM_011510929.1:c.669G>A
GALNT3 transcript variant X4	XM_047443883.1:c.669=	XM_047443883.1:c.669G>A
polypeptide N-acetylgalactosaminyltransferase 3	NP_004473.2:p.Val223=	NP_004473.2:p.Val223=
polypeptide N-acetylgalactosaminyltransferase 3 isoform X1	XP_005246506.1:p.Val223=	XP_005246506.1:p.Val223=
polypeptide N-acetylgalactosaminyltransferase 3 isoform X1	XP_016859259.1:p.Val223=	XP_016859259.1:p.Val223=
polypeptide N-acetylgalactosaminyltransferase 3 isoform X1	XP_011509231.1:p.Val223=	XP_011509231.1:p.Val223=
polypeptide N-acetylgalactosaminyltransferase 3 isoform X2	XP_047299839.1:p.Val223=	XP_047299839.1:p.Val223=

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#.

44 SubSNP, 12 Frequency, 2 ClinVar submissions

No	Submitter	Submission ID	Date (Build)
1	WUGSC_SSAHASNP	ss23100869	Apr 05, 2004 (121)
2	ILLUMINA	ss75033287	Dec 07, 2007 (129)
3	KRIBB_YJKIM	ss119839387	Dec 01, 2009 (131)
4	SEATTLESEQ	ss159702988	Dec 01, 2009 (131)
5	ILLUMINA	ss172421190	Jul 04, 2010 (132)
6	1000GENOMES	ss219632249	Jul 14, 2010 (132)
7	NHLBI-ESP	ss342084446	May 09, 2011 (134)
8	ILLUMINA	ss480654046	May 04, 2012 (137)
9	ILLUMINA	ss483948587	May 04, 2012 (137)
10	1000GENOMES	ss489838450	May 04, 2012 (137)
11	ILLUMINA	ss533867256	Sep 08, 2015 (146)
12	ILLUMINA	ss779218786	Sep 08, 2015 (146)
13	ILLUMINA	ss781284739	Sep 08, 2015 (146)
14	ILLUMINA	ss834684710	Sep 08, 2015 (146)
15	1000GENOMES	ss1300269041	Aug 21, 2014 (142)
16	EVA_EXAC	ss1686573504	Apr 01, 2015 (144)
17	WEILL_CORNELL_DGM	ss1920852789	Feb 12, 2016 (147)
18	ILLUMINA	ss1958475220	Feb 12, 2016 (147)
19	HUMAN_LONGEVITY	ss2236250249	Dec 20, 2016 (150)
20	ILLUMINA	ss2633699683	Nov 08, 2017 (151)
21	GNOMAD	ss2733077832	Nov 08, 2017 (151)
22	GNOMAD	ss2746806093	Nov 08, 2017 (151)
23	GNOMAD	ss2782366381	Nov 08, 2017 (151)
24	ILLUMINA	ss3022036315	Nov 08, 2017 (151)
25	ILLUMINA	ss3628212611	Oct 11, 2018 (152)
26	ILLUMINA	ss3631661602	Oct 11, 2018 (152)
27	ILLUMINA	ss3638299687	Oct 11, 2018 (152)
28	ILLUMINA	ss3643265793	Oct 11, 2018 (152)
29	ILLUMINA	ss3652479678	Oct 11, 2018 (152)
30	ILLUMINA	ss3725841707	Jul 13, 2019 (153)
31	PAGE_CC	ss3770961896	Jul 13, 2019 (153)
32	EVA	ss3823821575	Apr 25, 2020 (154)
33	SGDP_PRJ	ss3853889853	Apr 25, 2020 (154)
34	FSA-LAB	ss3984192577	Apr 26, 2021 (155)
35	EVA	ss3986202237	Apr 26, 2021 (155)
36	EVA	ss4017032070	Apr 26, 2021 (155)
37	TOPMED	ss4532366941	Apr 26, 2021 (155)
38	1000G_HIGH_COVERAGE	ss5250829155	Oct 12, 2022 (156)
39	EVA	ss5333846814	Oct 12, 2022 (156)
40	HUGCELL_USP	ss5450561409	Oct 12, 2022 (156)
41	1000G_HIGH_COVERAGE	ss5527546167	Oct 12, 2022 (156)
42	SANFORD_IMAGENETICS	ss5630274623	Oct 12, 2022 (156)
43	EVA	ss5933319700	Oct 12, 2022 (156)
44	EVA	ss5956496207	Oct 12, 2022 (156)
45	1000Genomes	NC_000002.11 - 166621413	Oct 11, 2018 (152)
46	1000Genomes_30x	NC_000002.12 - 165764903	Oct 12, 2022 (156)
47	ExAC	NC_000002.11 - 166621413	Oct 11, 2018 (152)
48	gnomAD - Genomes	NC_000002.12 - 165764903	Apr 26, 2021 (155)
49	gnomAD - Exomes	NC_000002.11 - 166621413	Jul 13, 2019 (153)
50	GO Exome Sequencing Project	NC_000002.11 - 166621413	Oct 11, 2018 (152)
51	HapMap	NC_000002.12 - 165764903	Apr 25, 2020 (154)
52	The PAGE Study	NC_000002.12 - 165764903	Jul 13, 2019 (153)
53	Qatari	NC_000002.11 - 166621413	Apr 25, 2020 (154)
54	SGDP_PRJ	NC_000002.11 - 166621413	Apr 25, 2020 (154)
55	TopMed	NC_000002.12 - 165764903	Apr 26, 2021 (155)
56	ALFA	NC_000002.12 - 165764903	Apr 26, 2021 (155)
57	ClinVar	RCV000361417.3	Oct 12, 2022 (156)
58	ClinVar	RCV000958588.6	Oct 12, 2022 (156)

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
ss483948587, ss3643265793	NC_000002.10:166329658:C:T	NC_000002.12:165764902:C:T	(self)
11320117, 6464946, 2136399, 280010, 2894719, 5906833, ss219632249, ss342084446, ss480654046, ss489838450, ss533867256, ss779218786, ss781284739, ss834684710, ss1300269041, ss1686573504, ss1920852789, ss1958475220, ss2633699683, ss2733077832, ss2746806093, ss2782366381, ss3022036315, ss3628212611, ss3631661602, ss3638299687, ss3652479678, ss3823821575, ss3853889853, ss3984192577, ss3986202237, ss4017032070, ss5333846814, ss5630274623, ss5956496207	NC_000002.11:166621412:C:T	NC_000002.12:165764902:C:T	(self)
RCV000361417.3, RCV000958588.6, 15072102, 80717746, 1940707, 183365, 336189820, 5436836166, ss2236250249, ss3725841707, ss3770961896, ss4532366941, ss5250829155, ss5450561409, ss5527546167, ss5933319700	NC_000002.12:165764902:C:T	NC_000002.12:165764902:C:T	(self)
ss23100869	NT_005403.14:16830829:C:T	NC_000002.12:165764902:C:T	(self)
ss75033287, ss119839387, ss159702988, ss172421190	NT_005403.17:16830830:C:T	NC_000002.12:165764902: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 rs13423840

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

rs13423840