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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.

rs564979861

Current Build 154

Released April 21, 2020

Organism
Homo sapiens
Position
chr3:120650841 (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=0.000024 (6/251386, GnomAD_exome)
T=0.000016 (2/125568, TOPMED)
T=0.000025 (3/121402, ExAC) (+ 4 more)
T=0.00003 (1/31394, GnomAD)
T=0.0002 (1/5008, 1000G)
T=0.0000 (0/2188, ALFA Project)
T=0.003 (3/998, GoNL)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
HGD : Missense Variant
Publications
0 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.120650841C>T
GRCh37.p13 chr 3 NC_000003.11:g.120369688C>T
HGD RefSeqGene NG_011957.1:g.36641G>A
Gene: HGD, homogentisate 1,2-dioxygenase (minus strand)
Molecule type Change Amino acid[Codon] SO Term
HGD transcript NM_000187.4:c.367G>A G [GGA] > R [AGA] Coding Sequence Variant
homogentisate 1,2-dioxygenase NP_000178.2:p.Gly123Arg G (Gly) > R (Arg) Missense Variant
HGD transcript variant X3 XM_017006277.2:c.-57= N/A 5 Prime UTR Variant
HGD transcript variant X1 XM_005247412.2:c.367G>A G [GGA] > R [AGA] Coding Sequence Variant
homogentisate 1,2-dioxygenase isoform X1 XP_005247469.1:p.Gly123Arg G (Gly) > R (Arg) Missense Variant
HGD transcript variant X2 XM_005247413.2:c.367G>A G [GGA] > R [AGA] Coding Sequence Variant
homogentisate 1,2-dioxygenase isoform X2 XP_005247470.1:p.Gly123Arg G (Gly) > R (Arg) Missense Variant
HGD transcript variant X4 XM_011512746.2:c.367G>A G [GGA] > R [AGA] Coding Sequence Variant
homogentisate 1,2-dioxygenase isoform X4 XP_011511048.1:p.Gly123Arg G (Gly) > R (Arg) Missense Variant
HGD transcript variant X5 XM_005247414.5:c.367G>A G [GGA] > R [AGA] Coding Sequence Variant
homogentisate 1,2-dioxygenase isoform X5 XP_005247471.1:p.Gly123Arg 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.

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 14898 C=0.99987 T=0.00013
European Sub 9824 C=0.9999 T=0.0001
African Sub 3372 C=1.0000 T=0.0000
African Others Sub 114 C=1.000 T=0.000
African American Sub 3258 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 736 C=0.999 T=0.001


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 251386 C=0.999976 T=0.000024
gnomAD - Exomes European Sub 135322 C=0.999963 T=0.000037
gnomAD - Exomes Asian Sub 49008 C=1.00000 T=0.00000
gnomAD - Exomes American Sub 34592 C=1.00000 T=0.00000
gnomAD - Exomes African Sub 16256 C=0.99994 T=0.00006
gnomAD - Exomes Ashkenazi Jewish Sub 10076 C=1.00000 T=0.00000
gnomAD - Exomes Other Sub 6132 C=1.0000 T=0.0000
TopMed Global Study-wide 125568 C=0.999984 T=0.000016
ExAC Global Study-wide 121402 C=0.999975 T=0.000025
ExAC Europe Sub 73346 C=0.99997 T=0.00003
ExAC Asian Sub 25164 C=1.00000 T=0.00000
ExAC American Sub 11578 C=1.00000 T=0.00000
ExAC African Sub 10406 C=0.99990 T=0.00010
ExAC Other Sub 908 C=1.000 T=0.000
gnomAD - Genomes Global Study-wide 31394 C=0.99997 T=0.00003
gnomAD - Genomes European Sub 18906 C=0.99995 T=0.00005
gnomAD - Genomes African Sub 8706 C=1.0000 T=0.0000
gnomAD - Genomes East Asian Sub 1556 C=1.0000 T=0.0000
gnomAD - Genomes Other Sub 1088 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
1000Genomes Global Study-wide 5008 C=0.9998 T=0.0002
1000Genomes African Sub 1322 C=0.9992 T=0.0008
1000Genomes East Asian Sub 1008 C=1.0000 T=0.0000
1000Genomes Europe Sub 1006 C=1.0000 T=0.0000
1000Genomes South Asian Sub 978 C=1.000 T=0.000
1000Genomes American Sub 694 C=1.000 T=0.000
ALFA Total Global 2188 C=1.0000 T=0.0000
ALFA European Sub 2072 C=1.0000 T=0.0000
ALFA African Sub 82 C=1.00 T=0.00
ALFA Other Sub 26 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
Genome of the Netherlands Release 5 Genome of the Netherlands Study-wide 998 C=0.997 T=0.003
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.120650841= NC_000003.12:g.120650841C>T
GRCh37.p13 chr 3 NC_000003.11:g.120369688= NC_000003.11:g.120369688C>T
HGD RefSeqGene NG_011957.1:g.36641= NG_011957.1:g.36641G>A
HGD transcript NM_000187.4:c.367= NM_000187.4:c.367G>A
HGD transcript NM_000187.3:c.367= NM_000187.3:c.367G>A
HGD transcript variant X5 XM_005247414.5:c.367= XM_005247414.5:c.367G>A
HGD transcript variant X3 XM_005247414.1:c.367= XM_005247414.1:c.367G>A
HGD transcript variant X3 XM_017006277.2:c.-57= XM_017006277.2:c.-57G>A
HGD transcript variant X1 XM_005247412.2:c.367= XM_005247412.2:c.367G>A
HGD transcript variant X1 XM_005247412.1:c.367= XM_005247412.1:c.367G>A
HGD transcript variant X2 XM_005247413.2:c.367= XM_005247413.2:c.367G>A
HGD transcript variant X2 XM_005247413.1:c.367= XM_005247413.1:c.367G>A
HGD transcript variant X4 XM_011512746.2:c.367= XM_011512746.2:c.367G>A
homogentisate 1,2-dioxygenase NP_000178.2:p.Gly123= NP_000178.2:p.Gly123Arg
homogentisate 1,2-dioxygenase isoform X5 XP_005247471.1:p.Gly123= XP_005247471.1:p.Gly123Arg
homogentisate 1,2-dioxygenase isoform X1 XP_005247469.1:p.Gly123= XP_005247469.1:p.Gly123Arg
homogentisate 1,2-dioxygenase isoform X2 XP_005247470.1:p.Gly123= XP_005247470.1:p.Gly123Arg
homogentisate 1,2-dioxygenase isoform X4 XP_011511048.1:p.Gly123= XP_011511048.1:p.Gly123Arg
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#.

12 SubSNP, 7 Frequency submissions
No Submitter Submission ID Date (Build)
1 EVA-GONL ss979083776 Aug 21, 2014 (142)
2 1000GENOMES ss1305859622 Aug 21, 2014 (142)
3 EVA_EXAC ss1687158455 Apr 01, 2015 (144)
4 HUMAN_LONGEVITY ss2255253621 Dec 20, 2016 (150)
5 TOPMED ss2422578055 Dec 20, 2016 (150)
6 GNOMAD ss2733990551 Nov 08, 2017 (151)
7 GNOMAD ss2747077609 Nov 08, 2017 (151)
8 GNOMAD ss2798280360 Nov 08, 2017 (151)
9 ILLUMINA ss3022278775 Nov 08, 2017 (151)
10 TOPMED ss3403599400 Nov 08, 2017 (151)
11 ILLUMINA ss3652757298 Oct 12, 2018 (152)
12 ILLUMINA ss3726050093 Jul 13, 2019 (153)
13 1000Genomes NC_000003.11 - 120369688 Oct 12, 2018 (152)
14 ExAC NC_000003.11 - 120369688 Oct 12, 2018 (152)
15 gnomAD - Genomes NC_000003.11 - 120369688 Jul 13, 2019 (153)
16 gnomAD - Exomes NC_000003.11 - 120369688 Jul 13, 2019 (153)
17 Genome of the Netherlands Release 5 NC_000003.11 - 120369688 Apr 25, 2020 (154)
18 TopMed NC_000003.12 - 120650841 Oct 12, 2018 (152)
19 dbGaP Population Frequency Project NC_000003.12 - 120650841 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
17112296, 7094384, 46815884, 3076041, 4187803, ss979083776, ss1305859622, ss1687158455, ss2422578055, ss2733990551, ss2747077609, ss2798280360, ss3022278775, ss3652757298 NC_000003.11:120369687:C:T NC_000003.12:120650840:C:T (self)
261521322, 474427973, ss2255253621, ss3403599400, ss3726050093 NC_000003.12:120650840:C:T NC_000003.12:120650840: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.

No publications for rs564979861

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