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dbSNP Short Genetic Variations

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.


Current Build 153

Released July 9, 2019

Homo sapiens
chr3:120674919 (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.

Variation Type
SNV Single Nucleotide Variation
T=0.00004 (10/251272, GnomAD_exome)
T=0.00004 (5/125568, TOPMED)
T=0.00002 (3/121336, ExAC)
Clinical Significance
Reported in ClinVar
Gene : Consequence
HGD : Missense Variant
2 citations
Genomic View
See rs on genome

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.120674919C>T
GRCh37.p13 chr 3 NC_000003.11:g.120393766C>T
HGD RefSeqGene NG_011957.1:g.12563G>A
Gene: HGD, homogentisate 1,2-dioxygenase (minus strand)
Molecule type Change Amino acid[Codon] SO Term
HGD transcript NM_000187.4:c.158G>A R [CGG] > Q [CAG] Coding Sequence Variant
homogentisate 1,2-dioxygenase NP_000178.2:p.Arg53Gln R (Arg) > Q (Gln) Missense Variant
HGD transcript variant X3 XM_017006277.2:c. N/A 5 Prime UTR Variant
HGD transcript variant X1 XM_005247412.2:c.158G>A R [CGG] > Q [CAG] Coding Sequence Variant
homogentisate 1,2-dioxygenase isoform X1 XP_005247469.1:p.Arg53Gln R (Arg) > Q (Gln) Missense Variant
HGD transcript variant X2 XM_005247413.2:c.158G>A R [CGG] > Q [CAG] Coding Sequence Variant
homogentisate 1,2-dioxygenase isoform X2 XP_005247470.1:p.Arg53Gln R (Arg) > Q (Gln) Missense Variant
HGD transcript variant X4 XM_011512746.2:c.158G>A R [CGG] > Q [CAG] Coding Sequence Variant
homogentisate 1,2-dioxygenase isoform X4 XP_011511048.1:p.Arg53Gln R (Arg) > Q (Gln) Missense Variant
HGD transcript variant X5 XM_005247414.5:c.158G>A R [CGG] > Q [CAG] Coding Sequence Variant
homogentisate 1,2-dioxygenase isoform X5 XP_005247471.1:p.Arg53Gln R (Arg) > Q (Gln) Missense 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: 357282 )
ClinVar Accession Disease Names Clinical Significance
RCV000412076.1 Alkaptonuria Likely-Pathogenic

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").

Study Population Group Sample Size Ref Allele Alt Allele
gnomAD - Exomes Global Study-wide 251272 C=0.99996 T=0.00004
gnomAD - Exomes European Sub 135262 C=0.99998 T=0.00002
gnomAD - Exomes Asian Sub 49000 C=0.9999 T=0.0001
gnomAD - Exomes American Sub 34560 C=0.9999 T=0.0001
gnomAD - Exomes African Sub 16250 C=1.0000 T=0.0000
gnomAD - Exomes Ashkenazi Jewish Sub 10068 C=1.0000 T=0.0000
gnomAD - Exomes Other Sub 6132 C=1.000 T=0.000
TopMed Global Study-wide 125568 C=0.99996 T=0.00004
ExAC Global Study-wide 121336 C=0.99998 T=0.00002
ExAC Europe Sub 73348 C=1.0000 T=0.0000
ExAC Asian Sub 25156 C=0.9999 T=0.0001
ExAC American Sub 11518 C=1.0000 T=0.0000
ExAC African Sub 10406 C=1.0000 T=0.0000
ExAC Other Sub 908 C=1.00 T=0.00

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 Note
GRCh38.p12 chr 3 NC_000003.12:g.120674919= NC_000003.12:g.12067491...


GRCh37.p13 chr 3 NC_000003.11:g.120393766= NC_000003.11:g.12039376...


HGD RefSeqGene NG_011957.1:g.12563= NG_011957.1:g.12563G>A
HGD transcript NM_000187.4:c.158= NM_000187.4:c.158G>A
HGD transcript NM_000187.3:c.158= NM_000187.3:c.158G>A
HGD transcript variant X5 XM_005247414.5:c.158= XM_005247414.5:c.158G>A
HGD transcript variant X3 XM_005247414.1:c.158= XM_005247414.1:c.158G>A
HGD transcript variant X3 XM_017006277.2:c.-266= XM_017006277.2:c.-266G>A
HGD transcript variant X1 XM_005247412.2:c.158= XM_005247412.2:c.158G>A
HGD transcript variant X1 XM_005247412.1:c.158= XM_005247412.1:c.158G>A
HGD transcript variant X2 XM_005247413.2:c.158= XM_005247413.2:c.158G>A
HGD transcript variant X2 XM_005247413.1:c.158= XM_005247413.1:c.158G>A
HGD transcript variant X4 XM_011512746.2:c.158= XM_011512746.2:c.158G>A
homogentisate 1,2-dioxygenase NP_000178.2:p.Arg53= NP_000178.2:p.Arg53Gln
homogentisate 1,2-dioxygenase isoform X5 XP_005247471.1:p.Arg53= XP_005247471.1:p.Arg53Gln
homogentisate 1,2-dioxygenase isoform X1 XP_005247469.1:p.Arg53= XP_005247469.1:p.Arg53Gln
homogentisate 1,2-dioxygenase isoform X2 XP_005247470.1:p.Arg53= XP_005247470.1:p.Arg53Gln
homogentisate 1,2-dioxygenase isoform X4 XP_011511048.1:p.Arg53= XP_011511048.1:p.Arg53Gln

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#.

5 SubSNP, 3 Frequency, 1 ClinVar submissions
No Submitter Submission ID Date (Build)
1 GMI ss277320438 May 04, 2012 (137)
2 EVA_EXAC ss1687158561 Apr 01, 2015 (144)
3 HUMAN_LONGEVITY ss2255255056 Dec 20, 2016 (150)
4 GNOMAD ss2733990687 Nov 08, 2017 (151)
5 TOPMED ss3403603598 Nov 08, 2017 (151)
6 ExAC NC_000003.11 - 120393766 Oct 12, 2018 (152)
7 gnomAD - Exomes NC_000003.11 - 120393766 Jul 13, 2019 (153)
8 TopMed NC_000003.12 - 120674919 Oct 12, 2018 (152)
9 ClinVar RCV000412076.1 Oct 12, 2018 (152)

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
ss277320438 NC_000003.10:121876455:C:T NC_000003.12:120674918:C:T (self)
7094495, 3076191, ss1687158561, ss2733990687 NC_000003.11:120393765:C:T NC_000003.12:120674918:C:T (self)
RCV000412076.1, 261524875, ss2255255056, ss3403603598 NC_000003.12:120674918:C:T NC_000003.12:120674918:C:T (self)

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

2 citations for rs200808744
PMID Title Author Year Journal
25681086 Analysis of HGD Gene Mutations in Patients with Alkaptonuria from the United Kingdom: Identification of Novel Mutations. Usher JL et al. 2015 JIMD reports
25804398 Twelve novel HGD gene variants identified in 99 alkaptonuria patients: focus on 'black bone disease' in Italy. Nemethova M et al. 2016 European journal of human genetics

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.post246+3cda961