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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.

rs369517993

Current Build 154

Released April 21, 2020

Organism
Homo sapiens
Position
chr3:120674937 (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
G>A / G>T
Variation Type
SNV Single Nucleotide Variation
Frequency
A=0.000004 (1/251280, GnomAD_exome)
A=0.000008 (1/125568, TOPMED)
T=0.000008 (1/121350, ExAC) (+ 5 more)
T=0.00006 (5/78680, PAGE_STUDY)
A=0.00000 (0/26266, ALFA Project)
T=0.00000 (0/26266, dbGaP Population Frequency Project)
T=0.00008 (1/12998, GO-ESP)
A=0.0002 (1/5008, 1000G)
Clinical Significance
Reported in ClinVar
Gene : Consequence
HGD : Stop Gained
Publications
1 citation
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.120674937G>A
GRCh38.p12 chr 3 NC_000003.12:g.120674937G>T
GRCh37.p13 chr 3 NC_000003.11:g.120393784G>A
GRCh37.p13 chr 3 NC_000003.11:g.120393784G>T
HGD RefSeqGene NG_011957.1:g.12545C>T
HGD RefSeqGene NG_011957.1:g.12545C>A
Gene: HGD, homogentisate 1,2-dioxygenase (minus strand)
Molecule type Change Amino acid[Codon] SO Term
HGD transcript NM_000187.4:c.140C>T S [TCG] > L [TTG] Coding Sequence Variant
homogentisate 1,2-dioxygenase NP_000178.2:p.Ser47Leu S (Ser) > L (Leu) Missense Variant
HGD transcript NM_000187.4:c.140C>A S [TCG] > * [TAG] Coding Sequence Variant
homogentisate 1,2-dioxygenase NP_000178.2:p.Ser47Ter S (Ser) > * (Ter) Stop Gained
HGD transcript variant X3 XM_017006277.2:c.-284= N/A 5 Prime UTR Variant
HGD transcript variant X1 XM_005247412.2:c.140C>T S [TCG] > L [TTG] Coding Sequence Variant
homogentisate 1,2-dioxygenase isoform X1 XP_005247469.1:p.Ser47Leu S (Ser) > L (Leu) Missense Variant
HGD transcript variant X1 XM_005247412.2:c.140C>A S [TCG] > * [TAG] Coding Sequence Variant
homogentisate 1,2-dioxygenase isoform X1 XP_005247469.1:p.Ser47Ter S (Ser) > * (Ter) Stop Gained
HGD transcript variant X2 XM_005247413.2:c.140C>T S [TCG] > L [TTG] Coding Sequence Variant
homogentisate 1,2-dioxygenase isoform X2 XP_005247470.1:p.Ser47Leu S (Ser) > L (Leu) Missense Variant
HGD transcript variant X2 XM_005247413.2:c.140C>A S [TCG] > * [TAG] Coding Sequence Variant
homogentisate 1,2-dioxygenase isoform X2 XP_005247470.1:p.Ser47Ter S (Ser) > * (Ter) Stop Gained
HGD transcript variant X4 XM_011512746.2:c.140C>T S [TCG] > L [TTG] Coding Sequence Variant
homogentisate 1,2-dioxygenase isoform X4 XP_011511048.1:p.Ser47Leu S (Ser) > L (Leu) Missense Variant
HGD transcript variant X4 XM_011512746.2:c.140C>A S [TCG] > * [TAG] Coding Sequence Variant
homogentisate 1,2-dioxygenase isoform X4 XP_011511048.1:p.Ser47Ter S (Ser) > * (Ter) Stop Gained
HGD transcript variant X5 XM_005247414.5:c.140C>T S [TCG] > L [TTG] Coding Sequence Variant
homogentisate 1,2-dioxygenase isoform X5 XP_005247471.1:p.Ser47Leu S (Ser) > L (Leu) Missense Variant
HGD transcript variant X5 XM_005247414.5:c.140C>A S [TCG] > * [TAG] Coding Sequence Variant
homogentisate 1,2-dioxygenase isoform X5 XP_005247471.1:p.Ser47Ter S (Ser) > * (Ter) Stop Gained
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: A (allele ID: 76482 )
ClinVar Accession Disease Names Clinical Significance
RCV000055778.1 Alkaptonuria Pathogenic

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 104026 G=1.000000 A=0.000000, T=0.000000
European Sub 92824 G=1.00000 A=0.00000, T=0.00000
African Sub 4188 G=1.0000 A=0.0000, T=0.0000
African Others Sub 168 G=1.000 A=0.000, T=0.000
African American Sub 4020 G=1.0000 A=0.0000, T=0.0000
Asian Sub 3308 G=1.0000 A=0.0000, T=0.0000
East Asian Sub 2682 G=1.0000 A=0.0000, T=0.0000
Other Asian Sub 626 G=1.000 A=0.000, T=0.000
Latin American 1 Sub 436 G=1.000 A=0.000, T=0.000
Latin American 2 Sub 928 G=1.000 A=0.000, T=0.000
South Asian Sub 280 G=1.000 A=0.000, T=0.000
Other Sub 2062 G=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
gnomAD - Exomes Global Study-wide 251280 G=0.999996 A=0.000004
gnomAD - Exomes European Sub 135254 G=1.000000 A=0.000000
gnomAD - Exomes Asian Sub 49006 G=0.99998 A=0.00002
gnomAD - Exomes American Sub 34566 G=1.00000 A=0.00000
gnomAD - Exomes African Sub 16250 G=1.00000 A=0.00000
gnomAD - Exomes Ashkenazi Jewish Sub 10072 G=1.00000 A=0.00000
gnomAD - Exomes Other Sub 6132 G=1.0000 A=0.0000
TopMed Global Study-wide 125568 G=0.999992 A=0.000008
ExAC Global Study-wide 121350 G=0.999992 T=0.000008
ExAC Europe Sub 73350 G=0.99999 T=0.00001
ExAC Asian Sub 25162 G=1.00000 T=0.00000
ExAC American Sub 11524 G=1.00000 T=0.00000
ExAC African Sub 10406 G=1.00000 T=0.00000
ExAC Other Sub 908 G=1.000 T=0.000
The PAGE Study Global Study-wide 78680 G=0.99994 T=0.00006
The PAGE Study AfricanAmerican Sub 32500 G=0.99991 T=0.00009
The PAGE Study Mexican Sub 10810 G=1.00000 T=0.00000
The PAGE Study Asian Sub 8318 G=1.0000 T=0.0000
The PAGE Study PuertoRican Sub 7916 G=0.9999 T=0.0001
The PAGE Study NativeHawaiian Sub 4532 G=0.9998 T=0.0002
The PAGE Study Cuban Sub 4230 G=1.0000 T=0.0000
The PAGE Study Dominican Sub 3826 G=1.0000 T=0.0000
The PAGE Study CentralAmerican Sub 2450 G=1.0000 T=0.0000
The PAGE Study SouthAmerican Sub 1982 G=1.0000 T=0.0000
The PAGE Study NativeAmerican Sub 1260 G=1.0000 T=0.0000
The PAGE Study SouthAsian Sub 856 G=1.000 T=0.000
ALFA Total Global 26266 G=1.00000 A=0.00000, T=0.00000
ALFA European Sub 25516 G=1.00000 A=0.00000, T=0.00000
ALFA Other Sub 556 G=1.000 A=0.000, T=0.000
ALFA African Sub 146 G=1.000 A=0.000, T=0.000
ALFA Asian Sub 38 G=1.00 A=0.00, T=0.00
ALFA South Asian Sub 10 G=1.0 A=0.0, T=0.0
ALFA Latin American 1 Sub 0 G=0 A=0, T=0
ALFA Latin American 2 Sub 0 G=0 A=0, T=0
GO Exome Sequencing Project Global Study-wide 12998 G=0.99992 T=0.00008
GO Exome Sequencing Project European American Sub 8592 G=0.9999 T=0.0001
GO Exome Sequencing Project African American Sub 4406 G=1.0000 T=0.0000
1000Genomes Global Study-wide 5008 G=0.9998 A=0.0002
1000Genomes African Sub 1322 G=1.0000 A=0.0000
1000Genomes East Asian Sub 1008 G=0.9990 A=0.0010
1000Genomes Europe Sub 1006 G=1.0000 A=0.0000
1000Genomes South Asian Sub 978 G=1.000 A=0.000
1000Genomes American Sub 694 G=1.000 A=0.000
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 G= A T
GRCh38.p12 chr 3 NC_000003.12:g.120674937= NC_000003.12:g.120674937G>A NC_000003.12:g.120674937G>T
GRCh37.p13 chr 3 NC_000003.11:g.120393784= NC_000003.11:g.120393784G>A NC_000003.11:g.120393784G>T
HGD RefSeqGene NG_011957.1:g.12545= NG_011957.1:g.12545C>T NG_011957.1:g.12545C>A
HGD transcript NM_000187.4:c.140= NM_000187.4:c.140C>T NM_000187.4:c.140C>A
HGD transcript NM_000187.3:c.140= NM_000187.3:c.140C>T NM_000187.3:c.140C>A
HGD transcript variant X5 XM_005247414.5:c.140= XM_005247414.5:c.140C>T XM_005247414.5:c.140C>A
HGD transcript variant X3 XM_005247414.1:c.140= XM_005247414.1:c.140C>T XM_005247414.1:c.140C>A
HGD transcript variant X3 XM_017006277.2:c.-284= XM_017006277.2:c.-284C>T XM_017006277.2:c.-284C>A
HGD transcript variant X1 XM_005247412.2:c.140= XM_005247412.2:c.140C>T XM_005247412.2:c.140C>A
HGD transcript variant X1 XM_005247412.1:c.140= XM_005247412.1:c.140C>T XM_005247412.1:c.140C>A
HGD transcript variant X2 XM_005247413.2:c.140= XM_005247413.2:c.140C>T XM_005247413.2:c.140C>A
HGD transcript variant X2 XM_005247413.1:c.140= XM_005247413.1:c.140C>T XM_005247413.1:c.140C>A
HGD transcript variant X4 XM_011512746.2:c.140= XM_011512746.2:c.140C>T XM_011512746.2:c.140C>A
homogentisate 1,2-dioxygenase NP_000178.2:p.Ser47= NP_000178.2:p.Ser47Leu NP_000178.2:p.Ser47Ter
homogentisate 1,2-dioxygenase isoform X5 XP_005247471.1:p.Ser47= XP_005247471.1:p.Ser47Leu XP_005247471.1:p.Ser47Ter
homogentisate 1,2-dioxygenase isoform X1 XP_005247469.1:p.Ser47= XP_005247469.1:p.Ser47Leu XP_005247469.1:p.Ser47Ter
homogentisate 1,2-dioxygenase isoform X2 XP_005247470.1:p.Ser47= XP_005247470.1:p.Ser47Leu XP_005247470.1:p.Ser47Ter
homogentisate 1,2-dioxygenase isoform X4 XP_011511048.1:p.Ser47= XP_011511048.1:p.Ser47Leu XP_011511048.1:p.Ser47Ter
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#.

18 SubSNP, 7 Frequency, 1 ClinVar submissions
No Submitter Submission ID Date (Build)
1 NHLBI-ESP ss712547083 Apr 25, 2013 (138)
2 CLINVAR ss836189081 Oct 23, 2013 (136)
3 1000GENOMES ss1305860303 Aug 21, 2014 (142)
4 EVA_EXAC ss1687158565 Apr 01, 2015 (144)
5 ILLUMINA ss1946093457 Feb 12, 2016 (147)
6 ILLUMINA ss1958598424 Feb 12, 2016 (147)
7 GNOMAD ss2733990691 Nov 08, 2017 (151)
8 AFFY ss2985267499 Nov 08, 2017 (151)
9 ILLUMINA ss3022278798 Nov 08, 2017 (151)
10 TOPMED ss3403603603 Nov 08, 2017 (151)
11 ILLUMINA ss3625824240 Oct 12, 2018 (152)
12 ILLUMINA ss3644826087 Oct 12, 2018 (152)
13 ILLUMINA ss3652757322 Oct 12, 2018 (152)
14 ILLUMINA ss3654036572 Oct 12, 2018 (152)
15 ILLUMINA ss3726050115 Jul 13, 2019 (153)
16 ILLUMINA ss3744221080 Jul 13, 2019 (153)
17 PAGE_CC ss3771058441 Jul 13, 2019 (153)
18 EVA ss3823945478 Apr 25, 2020 (154)
19 1000Genomes NC_000003.11 - 120393784 Oct 12, 2018 (152)
20 ExAC NC_000003.11 - 120393784 Oct 12, 2018 (152)
21 gnomAD - Exomes NC_000003.11 - 120393784 Jul 13, 2019 (153)
22 GO Exome Sequencing Project NC_000003.11 - 120393784 Oct 12, 2018 (152)
23 The PAGE Study NC_000003.12 - 120674937 Jul 13, 2019 (153)
24 TopMed NC_000003.12 - 120674937 Oct 12, 2018 (152)
25 dbGaP Population Frequency Project NC_000003.12 - 120674937 Apr 25, 2020 (154)
26 ClinVar RCV000055778.1 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
17113000, 3076195, ss1305860303 NC_000003.11:120393783:G:A NC_000003.12:120674936:G:A (self)
RCV000055778.1, 261524879, 930552689, ss836189081, ss3403603603 NC_000003.12:120674936:G:A NC_000003.12:120674936:G:A (self)
7094499, 403783, ss712547083, ss1687158565, ss1946093457, ss1958598424, ss2733990691, ss2985267499, ss3022278798, ss3625824240, ss3644826087, ss3652757322, ss3654036572, ss3744221080, ss3823945478 NC_000003.11:120393783:G:T NC_000003.12:120674936:G:T (self)
279910, 930552689, ss3726050115, ss3771058441 NC_000003.12:120674936:G:T NC_000003.12:120674936:G:T (self)
Help

Publications tab displays PubMed articles citing the variation as a listing of PMID, Title, Author, Year, Journal, ordered by Year, descending.

1 citation for rs369517993
PMID Title Author Year Journal
20301627 Alkaptonuria Introne WJ et al. 1993 GeneReviews®
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