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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.


Current Build 154

Released April 21, 2020

Homo sapiens
chr3:120647020 (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=0.000016 (4/251184, GnomAD_exome)
T=0.000048 (6/125568, TOPMED)
T=0.000025 (3/121322, ExAC) (+ 3 more)
T=0.00003 (1/31390, GnomAD)
T=0.00008 (1/12998, GO-ESP)
T=0.0000 (0/8578, ALFA Project)
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.120647020C>T
GRCh37.p13 chr 3 NC_000003.11:g.120365867C>T
HGD RefSeqGene NG_011957.1:g.40462G>A
Gene: HGD, homogentisate 1,2-dioxygenase (minus strand)
Molecule type Change Amino acid[Codon] SO Term
HGD transcript NM_000187.4:c.502G>A E [GAG] > K [AAG] Coding Sequence Variant
homogentisate 1,2-dioxygenase NP_000178.2:p.Glu168Lys E (Glu) > K (Lys) Missense Variant
HGD transcript variant X1 XM_005247412.2:c.502G>A E [GAG] > K [AAG] Coding Sequence Variant
homogentisate 1,2-dioxygenase isoform X1 XP_005247469.1:p.Glu168Lys E (Glu) > K (Lys) Missense Variant
HGD transcript variant X2 XM_005247413.2:c.502G>A E [GAG] > K [AAG] Coding Sequence Variant
homogentisate 1,2-dioxygenase isoform X2 XP_005247470.1:p.Glu168Lys E (Glu) > K (Lys) Missense Variant
HGD transcript variant X3 XM_017006277.2:c.79G>A E [GAG] > K [AAG] Coding Sequence Variant
homogentisate 1,2-dioxygenase isoform X3 XP_016861766.1:p.Glu27Lys E (Glu) > K (Lys) Missense Variant
HGD transcript variant X4 XM_011512746.2:c.502G>A E [GAG] > K [AAG] Coding Sequence Variant
homogentisate 1,2-dioxygenase isoform X4 XP_011511048.1:p.Glu168Lys E (Glu) > K (Lys) Missense Variant
HGD transcript variant X5 XM_005247414.5:c.502G>A E [GAG] > K [AAG] Coding Sequence Variant
homogentisate 1,2-dioxygenase isoform X5 XP_005247471.1:p.Glu168Lys E (Glu) > K (Lys) 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

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 20440 C=1.00000 T=0.00000
European Sub 15830 C=1.00000 T=0.00000
African Sub 2898 C=1.0000 T=0.0000
African Others Sub 114 C=1.000 T=0.000
African American Sub 2784 C=1.0000 T=0.0000
Asian Sub 112 C=1.000 T=0.000
East Asian Sub 86 C=1.00 T=0.00
Other Asian Sub 26 C=1.00 T=0.00
Latin American 1 Sub 146 C=1.000 T=0.000
Latin American 2 Sub 610 C=1.000 T=0.000
South Asian Sub 98 C=1.00 T=0.00
Other Sub 746 C=1.000 T=0.000


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 251184 C=0.999984 T=0.000016
gnomAD - Exomes European Sub 135142 C=0.999985 T=0.000015
gnomAD - Exomes Asian Sub 49004 C=0.99998 T=0.00002
gnomAD - Exomes American Sub 34584 C=1.00000 T=0.00000
gnomAD - Exomes African Sub 16256 C=0.99994 T=0.00006
gnomAD - Exomes Ashkenazi Jewish Sub 10068 C=1.00000 T=0.00000
gnomAD - Exomes Other Sub 6130 C=1.0000 T=0.0000
TopMed Global Study-wide 125568 C=0.999952 T=0.000048
ExAC Global Study-wide 121322 C=0.999975 T=0.000025
ExAC Europe Sub 73310 C=0.99997 T=0.00003
ExAC Asian Sub 25140 C=1.00000 T=0.00000
ExAC American Sub 11574 C=1.00000 T=0.00000
ExAC African Sub 10390 C=0.99990 T=0.00010
ExAC Other Sub 908 C=1.000 T=0.000
gnomAD - Genomes Global Study-wide 31390 C=0.99997 T=0.00003
gnomAD - Genomes European Sub 18892 C=1.00000 T=0.00000
gnomAD - Genomes African Sub 8716 C=0.9999 T=0.0001
gnomAD - Genomes East Asian Sub 1560 C=1.0000 T=0.0000
gnomAD - Genomes Other Sub 1084 C=1.0000 T=0.0000
gnomAD - Genomes American Sub 848 C=1.000 T=0.000
gnomAD - Genomes Ashkenazi Jewish Sub 290 C=1.000 T=0.000
GO Exome Sequencing Project Global Study-wide 12998 C=0.99992 T=0.00008
GO Exome Sequencing Project European American Sub 8592 C=1.0000 T=0.0000
GO Exome Sequencing Project African American Sub 4406 C=0.9998 T=0.0002
ALFA Total Global 8578 C=1.0000 T=0.0000
ALFA European Sub 8212 C=1.0000 T=0.0000
ALFA Other Sub 276 C=1.000 T=0.000
ALFA African Sub 82 C=1.00 T=0.00
ALFA South Asian Sub 4 C=1.0 T=0.0
ALFA Asian Sub 4 C=1.0 T=0.0
ALFA Latin American 1 Sub 0 C=0 T=0
ALFA Latin American 2 Sub 0 C=0 T=0

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.120647020= NC_000003.12:g.120647020C>T
GRCh37.p13 chr 3 NC_000003.11:g.120365867= NC_000003.11:g.120365867C>T
HGD RefSeqGene NG_011957.1:g.40462= NG_011957.1:g.40462G>A
HGD transcript NM_000187.4:c.502= NM_000187.4:c.502G>A
HGD transcript NM_000187.3:c.502= NM_000187.3:c.502G>A
HGD transcript variant X5 XM_005247414.5:c.502= XM_005247414.5:c.502G>A
HGD transcript variant X3 XM_005247414.1:c.502= XM_005247414.1:c.502G>A
HGD transcript variant X3 XM_017006277.2:c.79= XM_017006277.2:c.79G>A
HGD transcript variant X1 XM_005247412.2:c.502= XM_005247412.2:c.502G>A
HGD transcript variant X1 XM_005247412.1:c.502= XM_005247412.1:c.502G>A
HGD transcript variant X2 XM_005247413.2:c.502= XM_005247413.2:c.502G>A
HGD transcript variant X2 XM_005247413.1:c.502= XM_005247413.1:c.502G>A
HGD transcript variant X4 XM_011512746.2:c.502= XM_011512746.2:c.502G>A
homogentisate 1,2-dioxygenase NP_000178.2:p.Glu168= NP_000178.2:p.Glu168Lys
homogentisate 1,2-dioxygenase isoform X5 XP_005247471.1:p.Glu168= XP_005247471.1:p.Glu168Lys
homogentisate 1,2-dioxygenase isoform X3 XP_016861766.1:p.Glu27= XP_016861766.1:p.Glu27Lys
homogentisate 1,2-dioxygenase isoform X1 XP_005247469.1:p.Glu168= XP_005247469.1:p.Glu168Lys
homogentisate 1,2-dioxygenase isoform X2 XP_005247470.1:p.Glu168= XP_005247470.1:p.Glu168Lys
homogentisate 1,2-dioxygenase isoform X4 XP_011511048.1:p.Glu168= XP_011511048.1:p.Glu168Lys

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#.

11 SubSNP, 6 Frequency submissions
No Submitter Submission ID Date (Build)
1 NHLBI-ESP ss712547039 Apr 25, 2013 (138)
2 EVA_EXAC ss1687158401 Apr 01, 2015 (144)
3 TOPMED ss2422577826 Dec 20, 2016 (150)
4 GNOMAD ss2733990485 Nov 08, 2017 (151)
5 GNOMAD ss2747077587 Nov 08, 2017 (151)
6 GNOMAD ss2798280056 Nov 08, 2017 (151)
7 AFFY ss2985267484 Nov 08, 2017 (151)
8 TOPMED ss3403598713 Nov 08, 2017 (151)
9 ILLUMINA ss3625824235 Oct 12, 2018 (152)
10 ILLUMINA ss3654036556 Oct 12, 2018 (152)
11 EVA ss3823945426 Apr 25, 2020 (154)
12 ExAC NC_000003.11 - 120365867 Oct 12, 2018 (152)
13 gnomAD - Genomes NC_000003.11 - 120365867 Jul 13, 2019 (153)
14 gnomAD - Exomes NC_000003.11 - 120365867 Jul 13, 2019 (153)
15 GO Exome Sequencing Project NC_000003.11 - 120365867 Oct 12, 2018 (152)
16 TopMed NC_000003.12 - 120647020 Oct 12, 2018 (152)
17 dbGaP Population Frequency Project NC_000003.12 - 120647020 Apr 25, 2020 (154)

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
7094328, 46815580, 3075967, 403732, ss712547039, ss1687158401, ss2422577826, ss2733990485, ss2747077587, ss2798280056, ss2985267484, ss3625824235, ss3654036556, ss3823945426 NC_000003.11:120365866:C:T NC_000003.12:120647019:C:T (self)
261520749, 366586299, ss3403598713 NC_000003.12:120647019:C:T NC_000003.12:120647019:C:T (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 rs375283568


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.post565+e32b82c