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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.

rs143223637

Current Build 154

Released April 21, 2020

Organism
Homo sapiens
Position
chr3:120650876 (GRCh38.p12) 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 / C>T
Variation Type
SNV Single Nucleotide Variation
Frequency
T=0.005065 (636/125568, TOPMED)
T=0.00523 (68/12998, GO-ESP)
T=0.00036 (4/11176, ALFA Project) (+ 3 more)
T=0.0044 (22/5008, 1000G)
C=0.5 (3/6, SGDP_PRJ)
T=0.5 (3/6, SGDP_PRJ)
Clinical Significance
Reported in ClinVar
Gene : Consequence
HGD : 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.p12 chr 3 NC_000003.12:g.120650876C>A
GRCh38.p12 chr 3 NC_000003.12:g.120650876C>T
GRCh37.p13 chr 3 NC_000003.11:g.120369723C>A
GRCh37.p13 chr 3 NC_000003.11:g.120369723C>T
HGD RefSeqGene NG_011957.1:g.36606G>T
HGD RefSeqGene NG_011957.1:g.36606G>A
Gene: HGD, homogentisate 1,2-dioxygenase (minus strand)
Molecule type Change Amino acid[Codon] SO Term
HGD transcript NM_000187.4:c.343-11G>T N/A Intron Variant
HGD transcript variant X1 XM_005247412.2:c.343-11G>T N/A Intron Variant
HGD transcript variant X2 XM_005247413.2:c.343-11G>T N/A Intron Variant
HGD transcript variant X5 XM_005247414.5:c.343-11G>T N/A Intron Variant
HGD transcript variant X4 XM_011512746.2:c.343-11G>T N/A Intron Variant
HGD transcript variant X3 XM_017006277.2:c.-81-11G>T N/A Intron 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.

Allele: T (allele ID: 291944 )
ClinVar Accession Disease Names Clinical Significance
RCV000309641.1 Alkaptonuria Uncertain-Significance

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 23248 C=0.99978 A=0.00000, T=0.00022
European Sub 15752 C=1.00000 A=0.00000, T=0.00000
African Sub 3432 C=0.9985 A=0.0000, T=0.0015
African Others Sub 120 C=0.992 A=0.000, T=0.008
African American Sub 3312 C=0.9988 A=0.0000, T=0.0012
Asian Sub 172 C=1.000 A=0.000, T=0.000
East Asian Sub 114 C=1.000 A=0.000, T=0.000
Other Asian Sub 58 C=1.00 A=0.00, T=0.00
Latin American 1 Sub 154 C=1.000 A=0.000, T=0.000
Latin American 2 Sub 616 C=1.000 A=0.000, T=0.000
South Asian Sub 98 C=1.00 A=0.00, T=0.00
Other Sub 3024 C=1.0000 A=0.0000, T=0.0000


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 125568 C=0.994768 A=0.000167, T=0.005065
GO Exome Sequencing Project Global Study-wide 12998 C=0.99477 T=0.00523
GO Exome Sequencing Project European American Sub 8592 C=1.0000 T=0.0000
GO Exome Sequencing Project African American Sub 4406 C=0.9846 T=0.0154
ALFA Total Global 11176 C=0.99964 A=0.00000, T=0.00036
ALFA European Sub 8134 C=1.0000 A=0.0000, T=0.0000
ALFA Other Sub 2302 C=1.0000 A=0.0000, T=0.0000
ALFA African Sub 676 C=0.994 A=0.000, T=0.006
ALFA Asian Sub 60 C=1.00 A=0.00, T=0.00
ALFA South Asian Sub 4 C=1.0 A=0.0, T=0.0
ALFA Latin American 1 Sub 0 C=0 A=0, T=0
ALFA Latin American 2 Sub 0 C=0 A=0, T=0
1000Genomes Global Study-wide 5008 C=0.9950 A=0.0006, T=0.0044
1000Genomes African Sub 1322 C=0.9826 A=0.0023, T=0.0151
1000Genomes East Asian Sub 1008 C=1.0000 A=0.0000, T=0.0000
1000Genomes Europe Sub 1006 C=1.0000 A=0.0000, T=0.0000
1000Genomes South Asian Sub 978 C=1.000 A=0.000, T=0.000
1000Genomes American Sub 694 C=0.997 A=0.000, T=0.003
SGDP_PRJ Global Study-wide 6 C=0.5 T=0.5
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 C= A T
GRCh38.p12 chr 3 NC_000003.12:g.120650876= NC_000003.12:g.120650876C>A NC_000003.12:g.120650876C>T
GRCh37.p13 chr 3 NC_000003.11:g.120369723= NC_000003.11:g.120369723C>A NC_000003.11:g.120369723C>T
HGD RefSeqGene NG_011957.1:g.36606= NG_011957.1:g.36606G>T NG_011957.1:g.36606G>A
HGD transcript NM_000187.3:c.343-11= NM_000187.3:c.343-11G>T NM_000187.3:c.343-11G>A
HGD transcript NM_000187.4:c.343-11= NM_000187.4:c.343-11G>T NM_000187.4:c.343-11G>A
HGD transcript variant X1 XM_005247412.1:c.343-11= XM_005247412.1:c.343-11G>T XM_005247412.1:c.343-11G>A
HGD transcript variant X1 XM_005247412.2:c.343-11= XM_005247412.2:c.343-11G>T XM_005247412.2:c.343-11G>A
HGD transcript variant X2 XM_005247413.1:c.343-11= XM_005247413.1:c.343-11G>T XM_005247413.1:c.343-11G>A
HGD transcript variant X2 XM_005247413.2:c.343-11= XM_005247413.2:c.343-11G>T XM_005247413.2:c.343-11G>A
HGD transcript variant X3 XM_005247414.1:c.343-11= XM_005247414.1:c.343-11G>T XM_005247414.1:c.343-11G>A
HGD transcript variant X5 XM_005247414.5:c.343-11= XM_005247414.5:c.343-11G>T XM_005247414.5:c.343-11G>A
HGD transcript variant X4 XM_011512746.2:c.343-11= XM_011512746.2:c.343-11G>T XM_011512746.2:c.343-11G>A
HGD transcript variant X3 XM_017006277.2:c.-81-11= XM_017006277.2:c.-81-11G>T XM_017006277.2:c.-81-11G>A
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#.

23 SubSNP, 11 Frequency, 1 ClinVar submissions
No Submitter Submission ID Date (Build)
1 1000GENOMES ss331004760 May 09, 2011 (134)
2 1000GENOMES ss489894698 May 04, 2012 (137)
3 ILLUMINA ss534281249 Sep 08, 2015 (146)
4 TISHKOFF ss556900130 Apr 25, 2013 (138)
5 NHLBI-ESP ss712547048 Apr 25, 2013 (138)
6 JMKIDD_LAB ss1067454149 Aug 21, 2014 (142)
7 JMKIDD_LAB ss1070777261 Aug 21, 2014 (142)
8 1000GENOMES ss1305859626 Aug 21, 2014 (142)
9 1000GENOMES ss1305859627 Aug 21, 2014 (142)
10 EVA_EXAC ss1687158466 Apr 01, 2015 (144)
11 EVA_EXAC ss1687158467 Apr 01, 2015 (144)
12 HAMMER_LAB ss1799930642 Sep 08, 2015 (146)
13 HUMAN_LONGEVITY ss2255253624 Dec 20, 2016 (150)
14 TOPMED ss2422578058 Dec 20, 2016 (150)
15 TOPMED ss2422578059 Dec 20, 2016 (150)
16 GNOMAD ss2733990562 Nov 08, 2017 (151)
17 GNOMAD ss2747077614 Nov 08, 2017 (151)
18 GNOMAD ss2798280365 Nov 08, 2017 (151)
19 TOPMED ss3403599409 Nov 08, 2017 (151)
20 TOPMED ss3403599410 Nov 08, 2017 (151)
21 ILLUMINA ss3628759157 Oct 12, 2018 (152)
22 EVA ss3823945442 Apr 25, 2020 (154)
23 SGDP_PRJ ss3856813946 Apr 25, 2020 (154)
24 1000Genomes NC_000003.11 - 120369723 Oct 12, 2018 (152)
25 ExAC

Submission ignored due to conflicting rows:
Row 7094395 (NC_000003.11:120369722:C:C 121211/121382, NC_000003.11:120369722:C:T 171/121382)
Row 7094396 (NC_000003.11:120369722:C:C 121371/121382, NC_000003.11:120369722:C:A 11/121382)

- Oct 12, 2018 (152)
26 ExAC

Submission ignored due to conflicting rows:
Row 7094395 (NC_000003.11:120369722:C:C 121211/121382, NC_000003.11:120369722:C:T 171/121382)
Row 7094396 (NC_000003.11:120369722:C:C 121371/121382, NC_000003.11:120369722:C:A 11/121382)

- Oct 12, 2018 (152)
27 gnomAD - Genomes

Submission ignored due to conflicting rows:
Row 46815889 (NC_000003.11:120369722:C:C 31398/31404, NC_000003.11:120369722:C:A 6/31404)
Row 46815890 (NC_000003.11:120369722:C:C 31278/31404, NC_000003.11:120369722:C:T 126/31404)

- Jul 13, 2019 (153)
28 gnomAD - Genomes

Submission ignored due to conflicting rows:
Row 46815889 (NC_000003.11:120369722:C:C 31398/31404, NC_000003.11:120369722:C:A 6/31404)
Row 46815890 (NC_000003.11:120369722:C:C 31278/31404, NC_000003.11:120369722:C:T 126/31404)

- Jul 13, 2019 (153)
29 gnomAD - Exomes

Submission ignored due to conflicting rows:
Row 3076054 (NC_000003.11:120369722:C:C 251266/251292, NC_000003.11:120369722:C:A 26/251292)
Row 3076055 (NC_000003.11:120369722:C:C 251010/251292, NC_000003.11:120369722:C:T 282/251292)

- Jul 13, 2019 (153)
30 gnomAD - Exomes

Submission ignored due to conflicting rows:
Row 3076054 (NC_000003.11:120369722:C:C 251266/251292, NC_000003.11:120369722:C:A 26/251292)
Row 3076055 (NC_000003.11:120369722:C:C 251010/251292, NC_000003.11:120369722:C:T 282/251292)

- Jul 13, 2019 (153)
31 GO Exome Sequencing Project NC_000003.11 - 120369723 Oct 12, 2018 (152)
32 SGDP_PRJ NC_000003.11 - 120369723 Apr 25, 2020 (154)
33 TopMed NC_000003.12 - 120650876 Oct 12, 2018 (152)
34 dbGaP Population Frequency Project NC_000003.12 - 120650876 Apr 25, 2020 (154)
35 ClinVar RCV000309641.1 Oct 12, 2018 (152)
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
17112300, ss1305859626, ss1687158467, ss2422578058, ss2733990562, ss2747077614, ss2798280365 NC_000003.11:120369722:C:A NC_000003.12:120650875:C:A (self)
261521330, 375826633, ss2255253624, ss3403599409 NC_000003.12:120650875:C:A NC_000003.12:120650875:C:A (self)
17112300, 403747, 8830926, ss331004760, ss489894698, ss534281249, ss556900130, ss712547048, ss1067454149, ss1070777261, ss1305859627, ss1687158466, ss1799930642, ss2422578059, ss2733990562, ss2747077614, ss2798280365, ss3628759157, ss3823945442, ss3856813946 NC_000003.11:120369722:C:T NC_000003.12:120650875:C:T (self)
RCV000309641.1, 261521330, 375826633, ss2255253624, ss3403599410 NC_000003.12:120650875:C:T NC_000003.12:120650875:C:T (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 rs143223637

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.post557+f76c771