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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 155

Released April 9, 2021

Homo sapiens
chr3:120641636 (GRCh38.p13) 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
C=0.000042 (11/264690, TOPMED)
C=0.000048 (12/251408, GnomAD_exome)
C=0.000064 (9/140254, GnomAD) (+ 4 more)
C=0.000066 (8/121392, ExAC)
C=0.00008 (3/39902, ALFA)
C=0.00008 (1/13006, GO-ESP)
C=0.0002 (1/4480, Estonian)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
HGD : Missense Variant
0 citations
Genomic View
See rs on genome

ALFA Allele Frequency
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 39902 T=0.99992 C=0.00008
European Sub 31050 T=0.99990 C=0.00010
African Sub 2918 T=1.0000 C=0.0000
African Others Sub 114 T=1.000 C=0.000
African American Sub 2804 T=1.0000 C=0.0000
Asian Sub 112 T=1.000 C=0.000
East Asian Sub 86 T=1.00 C=0.00
Other Asian Sub 26 T=1.00 C=0.00
Latin American 1 Sub 500 T=1.000 C=0.000
Latin American 2 Sub 628 T=1.000 C=0.000
South Asian Sub 98 T=1.00 C=0.00
Other Sub 4596 T=1.0000 C=0.0000


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
TopMed Global Study-wide 264690 T=0.999958 C=0.000042
gnomAD - Exomes Global Study-wide 251408 T=0.999952 C=0.000048
gnomAD - Exomes European Sub 135342 T=0.999911 C=0.000089
gnomAD - Exomes Asian Sub 49006 T=1.00000 C=0.00000
gnomAD - Exomes American Sub 34590 T=1.00000 C=0.00000
gnomAD - Exomes African Sub 16256 T=1.00000 C=0.00000
gnomAD - Exomes Ashkenazi Jewish Sub 10078 T=1.00000 C=0.00000
gnomAD - Exomes Other Sub 6136 T=1.0000 C=0.0000
gnomAD - Genomes Global Study-wide 140254 T=0.999936 C=0.000064
gnomAD - Genomes European Sub 75942 T=0.99988 C=0.00012
gnomAD - Genomes African Sub 42040 T=1.00000 C=0.00000
gnomAD - Genomes American Sub 13660 T=1.00000 C=0.00000
gnomAD - Genomes Ashkenazi Jewish Sub 3324 T=1.0000 C=0.0000
gnomAD - Genomes East Asian Sub 3134 T=1.0000 C=0.0000
gnomAD - Genomes Other Sub 2154 T=1.0000 C=0.0000
ExAC Global Study-wide 121392 T=0.999934 C=0.000066
ExAC Europe Sub 73348 T=0.99989 C=0.00011
ExAC Asian Sub 25158 T=1.00000 C=0.00000
ExAC American Sub 11572 T=1.00000 C=0.00000
ExAC African Sub 10406 T=1.00000 C=0.00000
ExAC Other Sub 908 T=1.000 C=0.000
GO Exome Sequencing Project Global Study-wide 13006 T=0.99992 C=0.00008
GO Exome Sequencing Project European American Sub 8600 T=0.9999 C=0.0001
GO Exome Sequencing Project African American Sub 4406 T=1.0000 C=0.0000
Genetic variation in the Estonian population Estonian Study-wide 4480 T=0.9998 C=0.0002

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.p13 chr 3 NC_000003.12:g.120641636T>C
GRCh37.p13 chr 3 NC_000003.11:g.120360483T>C
HGD RefSeqGene NG_011957.1:g.45846A>G
Gene: HGD, homogentisate 1,2-dioxygenase (minus strand)
Molecule type Change Amino acid[Codon] SO Term
HGD transcript NM_000187.4:c.832A>G N [AAC] > D [GAC] Coding Sequence Variant
homogentisate 1,2-dioxygenase NP_000178.2:p.Asn278Asp N (Asn) > D (Asp) Missense Variant
HGD transcript variant X5 XM_005247414.5:c. N/A Genic Downstream Transcript Variant
HGD transcript variant X1 XM_005247412.2:c.607A>G N [AAC] > D [GAC] Coding Sequence Variant
homogentisate 1,2-dioxygenase isoform X1 XP_005247469.1:p.Asn203Asp N (Asn) > D (Asp) Missense Variant
HGD transcript variant X2 XM_005247413.2:c.832A>G N [AAC] > D [GAC] Coding Sequence Variant
homogentisate 1,2-dioxygenase isoform X2 XP_005247470.1:p.Asn278Asp N (Asn) > D (Asp) Missense Variant
HGD transcript variant X3 XM_017006277.2:c.409A>G N [AAC] > D [GAC] Coding Sequence Variant
homogentisate 1,2-dioxygenase isoform X3 XP_016861766.1:p.Asn137Asp N (Asn) > D (Asp) Missense Variant
HGD transcript variant X4 XM_011512746.2:c.832A>G N [AAC] > D [GAC] Coding Sequence Variant
homogentisate 1,2-dioxygenase isoform X4 XP_011511048.1:p.Asn278Asp N (Asn) > D (Asp) 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

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= C
GRCh38.p13 chr 3 NC_000003.12:g.120641636= NC_000003.12:g.120641636T>C
GRCh37.p13 chr 3 NC_000003.11:g.120360483= NC_000003.11:g.120360483T>C
HGD RefSeqGene NG_011957.1:g.45846= NG_011957.1:g.45846A>G
HGD transcript NM_000187.4:c.832= NM_000187.4:c.832A>G
HGD transcript NM_000187.3:c.832= NM_000187.3:c.832A>G
HGD transcript variant X3 XM_017006277.2:c.409= XM_017006277.2:c.409A>G
HGD transcript variant X1 XM_005247412.2:c.607= XM_005247412.2:c.607A>G
HGD transcript variant X1 XM_005247412.1:c.607= XM_005247412.1:c.607A>G
HGD transcript variant X2 XM_005247413.2:c.832= XM_005247413.2:c.832A>G
HGD transcript variant X2 XM_005247413.1:c.832= XM_005247413.1:c.832A>G
HGD transcript variant X4 XM_011512746.2:c.832= XM_011512746.2:c.832A>G
homogentisate 1,2-dioxygenase NP_000178.2:p.Asn278= NP_000178.2:p.Asn278Asp
homogentisate 1,2-dioxygenase isoform X3 XP_016861766.1:p.Asn137= XP_016861766.1:p.Asn137Asp
homogentisate 1,2-dioxygenase isoform X1 XP_005247469.1:p.Asn203= XP_005247469.1:p.Asn203Asp
homogentisate 1,2-dioxygenase isoform X2 XP_005247470.1:p.Asn278= XP_005247470.1:p.Asn278Asp
homogentisate 1,2-dioxygenase isoform X4 XP_011511048.1:p.Asn278= XP_011511048.1:p.Asn278Asp

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#.

10 SubSNP, 7 Frequency submissions
No Submitter Submission ID Date (Build)
1 NHLBI-ESP ss712547026 Apr 25, 2013 (138)
2 EVA_EXAC ss1687158286 Apr 01, 2015 (144)
3 HUMAN_LONGEVITY ss2255253126 Dec 20, 2016 (150)
4 GNOMAD ss2733990293 Nov 08, 2017 (151)
5 GNOMAD ss2747077545 Nov 08, 2017 (151)
6 GNOMAD ss2798279688 Nov 08, 2017 (151)
7 TOPMED ss3403597886 Nov 08, 2017 (151)
8 EGCUT_WGS ss3661001022 Jul 13, 2019 (153)
9 EVA ss3823945406 Apr 25, 2020 (154)
10 TOPMED ss4581090820 Apr 26, 2021 (155)
11 Genetic variation in the Estonian population NC_000003.11 - 120360483 Oct 12, 2018 (152)
12 ExAC NC_000003.11 - 120360483 Oct 12, 2018 (152)
13 gnomAD - Genomes NC_000003.12 - 120641636 Apr 26, 2021 (155)
14 gnomAD - Exomes NC_000003.11 - 120360483 Jul 13, 2019 (153)
15 GO Exome Sequencing Project NC_000003.11 - 120360483 Oct 12, 2018 (152)
16 TopMed NC_000003.12 - 120641636 Apr 26, 2021 (155)
17 ALFA NC_000003.12 - 120641636 Apr 26, 2021 (155)

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
6739270, 7094204, 3075764, 403713, ss712547026, ss1687158286, ss2733990293, ss2747077545, ss2798279688, ss3661001022, ss3823945406 NC_000003.11:120360482:T:C NC_000003.12:120641635:T:C (self)
121665107, 261520008, 418468375, 11882477301, ss2255253126, ss3403597886, ss4581090820 NC_000003.12:120641635:T:C NC_000003.12:120641635:T:C (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 rs370920635


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.post629+eb05767