Skip to main page content

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
chr3:120674952 (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
G=0.00004 (11/251268, GnomAD_exome)
G=0.00006 (8/125568, TOPMED)
G=0.00004 (5/121350, ExAC) (+ 5 more)
G=0.0000 (1/78700, PAGE_STUDY)
G=0.0000 (1/31398, GnomAD)
G=0.0002 (2/12998, GO-ESP)
G=0.000 (0/3854, ALSPAC)
G=0.000 (1/3708, TWINSUK)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
HGD : Missense Variant
0 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.120674952T>G
GRCh37.p13 chr 3 NC_000003.11:g.120393799T>G
HGD RefSeqGene NG_011957.1:g.12530A>C
Gene: HGD, homogentisate 1,2-dioxygenase (minus strand)
Molecule type Change Amino acid[Codon] SO Term
HGD transcript NM_000187.4:c.125A>C E [GAG] > A [GCG] Coding Sequence Variant
homogentisate 1,2-dioxygenase NP_000178.2:p.Glu42Ala E (Glu) > A (Ala) Missense Variant
HGD transcript variant X3 XM_017006277.2:c. N/A 5 Prime UTR Variant
HGD transcript variant X1 XM_005247412.2:c.125A>C E [GAG] > A [GCG] Coding Sequence Variant
homogentisate 1,2-dioxygenase isoform X1 XP_005247469.1:p.Glu42Ala E (Glu) > A (Ala) Missense Variant
HGD transcript variant X2 XM_005247413.2:c.125A>C E [GAG] > A [GCG] Coding Sequence Variant
homogentisate 1,2-dioxygenase isoform X2 XP_005247470.1:p.Glu42Ala E (Glu) > A (Ala) Missense Variant
HGD transcript variant X4 XM_011512746.2:c.125A>C E [GAG] > A [GCG] Coding Sequence Variant
homogentisate 1,2-dioxygenase isoform X4 XP_011511048.1:p.Glu42Ala E (Glu) > A (Ala) Missense Variant
HGD transcript variant X5 XM_005247414.5:c.125A>C E [GAG] > A [GCG] Coding Sequence Variant
homogentisate 1,2-dioxygenase isoform X5 XP_005247471.1:p.Glu42Ala E (Glu) > A (Ala) 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.

Not Reported in ClinVar

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 251268 T=0.99996 G=0.00004
gnomAD - Exomes European Sub 135250 T=0.99993 G=0.00007
gnomAD - Exomes Asian Sub 49006 T=1.0000 G=0.0000
gnomAD - Exomes American Sub 34560 T=1.0000 G=0.0000
gnomAD - Exomes African Sub 16250 T=0.9999 G=0.0001
gnomAD - Exomes Ashkenazi Jewish Sub 10074 T=1.0000 G=0.0000
gnomAD - Exomes Other Sub 6128 T=1.000 G=0.000
TopMed Global Study-wide 125568 T=0.99994 G=0.00006
ExAC Global Study-wide 121350 T=0.99996 G=0.00004
ExAC Europe Sub 73348 T=0.9999 G=0.0001
ExAC Asian Sub 25164 T=1.0000 G=0.0000
ExAC American Sub 11524 T=1.0000 G=0.0000
ExAC African Sub 10406 T=1.0000 G=0.0000
ExAC Other Sub 908 T=1.00 G=0.00
The PAGE Study Global Study-wide 78700 T=1.0000 G=0.0000
The PAGE Study AfricanAmerican Sub 32516 T=1.0000 G=0.0000
The PAGE Study Mexican Sub 10810 T=1.0000 G=0.0000
The PAGE Study Asian Sub 8316 T=1.000 G=0.000
The PAGE Study PuertoRican Sub 7918 T=1.000 G=0.000
The PAGE Study NativeHawaiian Sub 4534 T=1.000 G=0.000
The PAGE Study Cuban Sub 4230 T=1.000 G=0.000
The PAGE Study Dominican Sub 3828 T=1.000 G=0.000
The PAGE Study CentralAmerican Sub 2450 T=1.000 G=0.000
The PAGE Study SouthAmerican Sub 1982 T=1.000 G=0.000
The PAGE Study NativeAmerican Sub 1260 T=1.000 G=0.000
The PAGE Study SouthAsian Sub 856 T=1.00 G=0.00
gnomAD - Genomes Global Study-wide 31398 T=1.0000 G=0.0000
gnomAD - Genomes European Sub 18900 T=0.9999 G=0.0001
gnomAD - Genomes African Sub 8714 T=1.000 G=0.000
gnomAD - Genomes East Asian Sub 1560 T=1.000 G=0.000
gnomAD - Genomes Other Sub 1086 T=1.000 G=0.000
gnomAD - Genomes American Sub 848 T=1.00 G=0.00
gnomAD - Genomes Ashkenazi Jewish Sub 290 T=1.00 G=0.00
GO Exome Sequencing Project Global Study-wide 12998 T=0.9998 G=0.0002
GO Exome Sequencing Project European American Sub 8592 T=1.000 G=0.000
GO Exome Sequencing Project African American Sub 4406 T=1.000 G=0.000
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 T=1.000 G=0.000
UK 10K study - Twins TWIN COHORT Study-wide 3708 T=1.000 G=0.000

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 T= G Note
GRCh38.p12 chr 3 NC_000003.12:g.120674952= NC_000003.12:g.12067495...


GRCh37.p13 chr 3 NC_000003.11:g.120393799= NC_000003.11:g.12039379...


HGD RefSeqGene NG_011957.1:g.12530= NG_011957.1:g.12530A>C
HGD transcript NM_000187.4:c.125= NM_000187.4:c.125A>C
HGD transcript NM_000187.3:c.125= NM_000187.3:c.125A>C
HGD transcript variant X5 XM_005247414.5:c.125= XM_005247414.5:c.125A>C
HGD transcript variant X3 XM_005247414.1:c.125= XM_005247414.1:c.125A>C
HGD transcript variant X3 XM_017006277.2:c.-299= XM_017006277.2:c.-299A>C
HGD transcript variant X1 XM_005247412.2:c.125= XM_005247412.2:c.125A>C
HGD transcript variant X1 XM_005247412.1:c.125= XM_005247412.1:c.125A>C
HGD transcript variant X2 XM_005247413.2:c.125= XM_005247413.2:c.125A>C
HGD transcript variant X2 XM_005247413.1:c.125= XM_005247413.1:c.125A>C
HGD transcript variant X4 XM_011512746.2:c.125= XM_011512746.2:c.125A>C
homogentisate 1,2-dioxygenase NP_000178.2:p.Glu42= NP_000178.2:p.Glu42Ala
homogentisate 1,2-dioxygenase isoform X5 XP_005247471.1:p.Glu42= XP_005247471.1:p.Glu42Ala
homogentisate 1,2-dioxygenase isoform X1 XP_005247469.1:p.Glu42= XP_005247469.1:p.Glu42Ala
homogentisate 1,2-dioxygenase isoform X2 XP_005247470.1:p.Glu42= XP_005247470.1:p.Glu42Ala
homogentisate 1,2-dioxygenase isoform X4 XP_011511048.1:p.Glu42= XP_011511048.1:p.Glu42Ala

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#.

20 SubSNP, 8 Frequency submissions
No Submitter Submission ID Date (Build)
1 NHLBI-ESP ss712547084 Apr 25, 2013 (138)
2 EVA_UK10K_ALSPAC ss1608059794 Apr 01, 2015 (144)
3 EVA_UK10K_TWINSUK ss1651053827 Apr 01, 2015 (144)
4 EVA_EXAC ss1687158570 Apr 01, 2015 (144)
5 ILLUMINA ss1946093458 Feb 12, 2016 (147)
6 ILLUMINA ss1958598425 Feb 12, 2016 (147)
7 HUMAN_LONGEVITY ss2255255062 Dec 20, 2016 (150)
8 GNOMAD ss2733990698 Nov 08, 2017 (151)
9 GNOMAD ss2747077663 Nov 08, 2017 (151)
10 GNOMAD ss2798282140 Nov 08, 2017 (151)
11 AFFY ss2985267500 Nov 08, 2017 (151)
12 ILLUMINA ss3022278799 Nov 08, 2017 (151)
13 TOPMED ss3403603608 Nov 08, 2017 (151)
14 ILLUMINA ss3625824241 Oct 12, 2018 (152)
15 ILLUMINA ss3644826088 Oct 12, 2018 (152)
16 ILLUMINA ss3652757323 Oct 12, 2018 (152)
17 ILLUMINA ss3654036573 Oct 12, 2018 (152)
18 ILLUMINA ss3726050116 Jul 13, 2019 (153)
19 ILLUMINA ss3744221081 Jul 13, 2019 (153)
20 PAGE_CC ss3771058442 Jul 13, 2019 (153)
21 The Avon Longitudinal Study of Parents and Children NC_000003.11 - 120393799 Oct 12, 2018 (152)
22 ExAC NC_000003.11 - 120393799 Oct 12, 2018 (152)
23 gnomAD - Genomes NC_000003.11 - 120393799 Jul 13, 2019 (153)
24 gnomAD - Exomes NC_000003.11 - 120393799 Jul 13, 2019 (153)
25 GO Exome Sequencing Project NC_000003.11 - 120393799 Oct 12, 2018 (152)
26 The PAGE Study NC_000003.12 - 120674952 Jul 13, 2019 (153)
27 TopMed NC_000003.12 - 120674952 Oct 12, 2018 (152)
28 UK 10K study - Twins NC_000003.11 - 120393799 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
9532729, 7094504, 46817689, 3076203, 403785, 9532729, ss712547084, ss1608059794, ss1651053827, ss1687158570, ss1946093458, ss1958598425, ss2733990698, ss2747077663, ss2798282140, ss2985267500, ss3022278799, ss3625824241, ss3644826088, ss3652757323, ss3654036573, ss3744221081 NC_000003.11:120393798:T:G NC_000003.12:120674951:T:G (self)
279911, 261524884, ss2255255062, ss3403603608, ss3726050116, ss3771058442 NC_000003.12:120674951:T:G NC_000003.12:120674951:T:G (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 rs373921680

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