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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.

rs28941783

Current Build 154

Released April 21, 2020

Organism
Homo sapiens
Position
chr3:120647041 (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>T
Variation Type
SNV Single Nucleotide Variation
Frequency
T=0.000088 (22/251104, GnomAD_exome)
T=0.000135 (17/125568, TOPMED)
T=0.000124 (15/121252, ExAC) (+ 3 more)
T=0.00027 (13/48702, ALFA Project)
T=0.00045 (14/31390, GnomAD)
T=0.0027 (12/4480, Estonian)
Clinical Significance
Reported in ClinVar
Gene : Consequence
HGD : Missense Variant
Publications
6 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.120647041C>T
GRCh37.p13 chr 3 NC_000003.11:g.120365888C>T
HGD RefSeqGene NG_011957.1:g.40441G>A
Gene: HGD, homogentisate 1,2-dioxygenase (minus strand)
Molecule type Change Amino acid[Codon] SO Term
HGD transcript NM_000187.4:c.481G>A G [GGG] > R [AGG] Coding Sequence Variant
homogentisate 1,2-dioxygenase NP_000178.2:p.Gly161Arg G (Gly) > R (Arg) Missense Variant
HGD transcript variant X1 XM_005247412.2:c.481G>A G [GGG] > R [AGG] Coding Sequence Variant
homogentisate 1,2-dioxygenase isoform X1 XP_005247469.1:p.Gly161Arg G (Gly) > R (Arg) Missense Variant
HGD transcript variant X2 XM_005247413.2:c.481G>A G [GGG] > R [AGG] Coding Sequence Variant
homogentisate 1,2-dioxygenase isoform X2 XP_005247470.1:p.Gly161Arg G (Gly) > R (Arg) Missense Variant
HGD transcript variant X3 XM_017006277.2:c.58G>A G [GGG] > R [AGG] Coding Sequence Variant
homogentisate 1,2-dioxygenase isoform X3 XP_016861766.1:p.Gly20Arg G (Gly) > R (Arg) Missense Variant
HGD transcript variant X4 XM_011512746.2:c.481G>A G [GGG] > R [AGG] Coding Sequence Variant
homogentisate 1,2-dioxygenase isoform X4 XP_011511048.1:p.Gly161Arg G (Gly) > R (Arg) Missense Variant
HGD transcript variant X5 XM_005247414.5:c.481G>A G [GGG] > R [AGG] Coding Sequence Variant
homogentisate 1,2-dioxygenase isoform X5 XP_005247471.1:p.Gly161Arg G (Gly) > R (Arg) Missense 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: 18207 )
ClinVar Accession Disease Names Clinical Significance
RCV000003318.7 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 152308 C=0.999698 T=0.000302
European Sub 131686 C=0.999666 T=0.000334
African Sub 4280 C=1.0000 T=0.0000
African Others Sub 168 C=1.000 T=0.000
African American Sub 4112 C=1.0000 T=0.0000
Asian Sub 3334 C=1.0000 T=0.0000
East Asian Sub 2682 C=1.0000 T=0.0000
Other Asian Sub 652 C=1.000 T=0.000
Latin American 1 Sub 790 C=1.000 T=0.000
Latin American 2 Sub 946 C=1.000 T=0.000
South Asian Sub 280 C=1.000 T=0.000
Other Sub 10992 C=0.99982 T=0.00018


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 251104 C=0.999912 T=0.000088
gnomAD - Exomes European Sub 135080 C=0.999852 T=0.000148
gnomAD - Exomes Asian Sub 48992 C=1.00000 T=0.00000
gnomAD - Exomes American Sub 34582 C=0.99997 T=0.00003
gnomAD - Exomes African Sub 16256 C=1.00000 T=0.00000
gnomAD - Exomes Ashkenazi Jewish Sub 10068 C=1.00000 T=0.00000
gnomAD - Exomes Other Sub 6126 C=0.9998 T=0.0002
TopMed Global Study-wide 125568 C=0.999865 T=0.000135
ExAC Global Study-wide 121252 C=0.999876 T=0.000124
ExAC Europe Sub 73276 C=0.99981 T=0.00019
ExAC Asian Sub 25124 C=1.00000 T=0.00000
ExAC American Sub 11566 C=1.00000 T=0.00000
ExAC African Sub 10378 C=1.00000 T=0.00000
ExAC Other Sub 908 C=0.999 T=0.001
ALFA Total Global 48702 C=0.99973 T=0.00027
ALFA European Sub 43024 C=0.99974 T=0.00026
ALFA Other Sub 5336 C=0.9996 T=0.0004
ALFA African Sub 218 C=1.000 T=0.000
ALFA Asian Sub 110 C=1.000 T=0.000
ALFA South Asian Sub 14 C=1.00 T=0.00
ALFA Latin American 1 Sub 0 C=0 T=0
ALFA Latin American 2 Sub 0 C=0 T=0
gnomAD - Genomes Global Study-wide 31390 C=0.99955 T=0.00045
gnomAD - Genomes European Sub 18886 C=0.99931 T=0.00069
gnomAD - Genomes African Sub 8718 C=1.0000 T=0.0000
gnomAD - Genomes East Asian Sub 1560 C=1.0000 T=0.0000
gnomAD - Genomes Other Sub 1088 C=0.9991 T=0.0009
gnomAD - Genomes American Sub 848 C=1.000 T=0.000
gnomAD - Genomes Ashkenazi Jewish Sub 290 C=1.000 T=0.000
Genetic variation in the Estonian population Estonian Study-wide 4480 C=0.9973 T=0.0027
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= T
GRCh38.p12 chr 3 NC_000003.12:g.120647041= NC_000003.12:g.120647041C>T
GRCh37.p13 chr 3 NC_000003.11:g.120365888= NC_000003.11:g.120365888C>T
HGD RefSeqGene NG_011957.1:g.40441= NG_011957.1:g.40441G>A
HGD transcript NM_000187.4:c.481= NM_000187.4:c.481G>A
HGD transcript NM_000187.3:c.481= NM_000187.3:c.481G>A
HGD transcript variant X5 XM_005247414.5:c.481= XM_005247414.5:c.481G>A
HGD transcript variant X3 XM_005247414.1:c.481= XM_005247414.1:c.481G>A
HGD transcript variant X3 XM_017006277.2:c.58= XM_017006277.2:c.58G>A
HGD transcript variant X1 XM_005247412.2:c.481= XM_005247412.2:c.481G>A
HGD transcript variant X1 XM_005247412.1:c.481= XM_005247412.1:c.481G>A
HGD transcript variant X2 XM_005247413.2:c.481= XM_005247413.2:c.481G>A
HGD transcript variant X2 XM_005247413.1:c.481= XM_005247413.1:c.481G>A
HGD transcript variant X4 XM_011512746.2:c.481= XM_011512746.2:c.481G>A
homogentisate 1,2-dioxygenase NP_000178.2:p.Gly161= NP_000178.2:p.Gly161Arg
homogentisate 1,2-dioxygenase isoform X5 XP_005247471.1:p.Gly161= XP_005247471.1:p.Gly161Arg
homogentisate 1,2-dioxygenase isoform X3 XP_016861766.1:p.Gly20= XP_016861766.1:p.Gly20Arg
homogentisate 1,2-dioxygenase isoform X1 XP_005247469.1:p.Gly161= XP_005247469.1:p.Gly161Arg
homogentisate 1,2-dioxygenase isoform X2 XP_005247470.1:p.Gly161= XP_005247470.1:p.Gly161Arg
homogentisate 1,2-dioxygenase isoform X4 XP_011511048.1:p.Gly161= XP_011511048.1:p.Gly161Arg
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#.

22 SubSNP, 6 Frequency, 1 ClinVar submissions
No Submitter Submission ID Date (Build)
1 OMIM-CURATED-RECORDS ss255605789 Aug 20, 2010 (132)
2 NHLBI-ESP ss342144231 May 09, 2011 (134)
3 EXOME_CHIP ss491344687 May 04, 2012 (137)
4 ILLUMINA ss780820714 Sep 08, 2015 (146)
5 ILLUMINA ss783503131 Sep 08, 2015 (146)
6 EVA_EXAC ss1687158406 Apr 01, 2015 (144)
7 ILLUMINA ss1752435079 Sep 08, 2015 (146)
8 ILLUMINA ss1917771370 Feb 12, 2016 (147)
9 ILLUMINA ss1946093448 Feb 12, 2016 (147)
10 HUMAN_LONGEVITY ss2255253412 Dec 20, 2016 (150)
11 GNOMAD ss2733990490 Nov 08, 2017 (151)
12 GNOMAD ss2747077589 Nov 08, 2017 (151)
13 GNOMAD ss2798280058 Nov 08, 2017 (151)
14 ILLUMINA ss3022278767 Nov 08, 2017 (151)
15 TOPMED ss3403598717 Nov 08, 2017 (151)
16 ILLUMINA ss3628759149 Oct 12, 2018 (152)
17 ILLUMINA ss3652757290 Oct 12, 2018 (152)
18 EGCUT_WGS ss3661001088 Jul 13, 2019 (153)
19 ILLUMINA ss3726050086 Jul 13, 2019 (153)
20 ILLUMINA ss3744514707 Jul 13, 2019 (153)
21 ILLUMINA ss3772708646 Jul 13, 2019 (153)
22 EVA ss3823945429 Apr 25, 2020 (154)
23 Genetic variation in the Estonian population NC_000003.11 - 120365888 Oct 12, 2018 (152)
24 ExAC NC_000003.11 - 120365888 Oct 12, 2018 (152)
25 gnomAD - Genomes NC_000003.11 - 120365888 Jul 13, 2019 (153)
26 gnomAD - Exomes NC_000003.11 - 120365888 Jul 13, 2019 (153)
27 TopMed NC_000003.12 - 120647041 Oct 12, 2018 (152)
28 dbGaP Population Frequency Project NC_000003.12 - 120647041 Apr 25, 2020 (154)
29 ClinVar RCV000003318.7 Apr 25, 2020 (154)
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
6739336, 7094333, 46815582, 3075972, ss342144231, ss491344687, ss780820714, ss783503131, ss1687158406, ss1752435079, ss1917771370, ss1946093448, ss2733990490, ss2747077589, ss2798280058, ss3022278767, ss3628759149, ss3652757290, ss3661001088, ss3744514707, ss3772708646, ss3823945429 NC_000003.11:120365887:C:T NC_000003.12:120647040:C:T (self)
RCV000003318.7, 261520753, 50960450, ss255605789, ss2255253412, ss3403598717, ss3726050086 NC_000003.12:120647040:C:T NC_000003.12:120647040: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.

6 citations for rs28941783
PMID Title Author Year Journal
9154114 Molecular defects in alkaptonuria. Gehrig A et al. 1997 Cytogenetics and cell genetics
10482952 Allelic heterogeneity of alkaptonuria in Central Europe. Müller CR et al. 1999 European journal of human genetics
10970188 Novel mutations in the homogentisate-1,2-dioxygenase gene identified in Slovak patients with alkaptonuria. Zatková A et al. 2000 Journal of medical genetics
12051967 Alkaptonuria in Slovakia: thirty-two years of research on phenotype and genotype. Srsen S et al. 2002 Molecular genetics and metabolism
20301627 Alkaptonuria Introne WJ et al. 1993 GeneReviews®
22606059 Computational methods to work as first-pass filter in deleterious SNP analysis of alkaptonuria. Magesh R et al. 2012 TheScientificWorldJournal
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