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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.

rs397515346

Current Build 154

Released April 21, 2020

Organism
Homo sapiens
Position
chr3:120647889-120647892 (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
dupC
Variation Type
Indel Insertion and Deletion
Frequency
dupC=0.000028 (7/251278, GnomAD_exome)
dupC=0.000024 (3/125568, TOPMED)
dupC=0.000049 (6/121384, ExAC) (+ 3 more)
dupC=0.00010 (3/31402, GnomAD)
dupC=0.00008 (1/12512, GO-ESP)
dupC=0.0005 (1/2188, ALFA Project)
Clinical Significance
Reported in ClinVar
Gene : Consequence
HGD : Frameshift Variant
Publications
2 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.120647892dup
GRCh37.p13 chr 3 NC_000003.11:g.120366739dup
HGD RefSeqGene NG_011957.1:g.39593dup
Gene: HGD, homogentisate 1,2-dioxygenase (minus strand)
Molecule type Change Amino acid[Codon] SO Term
HGD transcript NM_000187.4:c.457dup D [GAC] > G [GGAC] Coding Sequence Variant
homogentisate 1,2-dioxygenase NP_000178.2:p.Asp153fs D (Asp) > G (Gly) Frameshift Variant
HGD transcript variant X1 XM_005247412.2:c.457dup D [GAC] > G [GGAC] Coding Sequence Variant
homogentisate 1,2-dioxygenase isoform X1 XP_005247469.1:p.Asp153fs D (Asp) > G (Gly) Frameshift Variant
HGD transcript variant X2 XM_005247413.2:c.457dup D [GAC] > G [GGAC] Coding Sequence Variant
homogentisate 1,2-dioxygenase isoform X2 XP_005247470.1:p.Asp153fs D (Asp) > G (Gly) Frameshift Variant
HGD transcript variant X3 XM_017006277.2:c.34dup D [GAC] > G [GGAC] Coding Sequence Variant
homogentisate 1,2-dioxygenase isoform X3 XP_016861766.1:p.Asp12fs D (Asp) > G (Gly) Frameshift Variant
HGD transcript variant X4 XM_011512746.2:c.457dup D [GAC] > G [GGAC] Coding Sequence Variant
homogentisate 1,2-dioxygenase isoform X4 XP_011511048.1:p.Asp153fs D (Asp) > G (Gly) Frameshift Variant
HGD transcript variant X5 XM_005247414.5:c.457dup D [GAC] > G [GGAC] Coding Sequence Variant
homogentisate 1,2-dioxygenase isoform X5 XP_005247471.1:p.Asp153fs D (Asp) > G (Gly) Frameshift 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.

Allele: dupC (allele ID: 18208 )
ClinVar Accession Disease Names Clinical Significance
RCV000003319.6 Alkaptonuria Pathogenic

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 14050 CCCC=0.99986 CCCCC=0.00014
European Sub 9690 CCCC=0.9999 CCCCC=0.0001
African Sub 2898 CCCC=1.0000 CCCCC=0.0000
African Others Sub 114 CCCC=1.000 CCCCC=0.000
African American Sub 2784 CCCC=1.0000 CCCCC=0.0000
Asian Sub 112 CCCC=1.000 CCCCC=0.000
East Asian Sub 86 CCCC=1.00 CCCCC=0.00
Other Asian Sub 26 CCCC=1.00 CCCCC=0.00
Latin American 1 Sub 146 CCCC=1.000 CCCCC=0.000
Latin American 2 Sub 610 CCCC=1.000 CCCCC=0.000
South Asian Sub 98 CCCC=1.00 CCCCC=0.00
Other Sub 496 CCCC=0.998 CCCCC=0.002


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 251278 -

No frequency provided

dupC=0.000028
gnomAD - Exomes European Sub 135218 -

No frequency provided

dupC=0.000030
gnomAD - Exomes Asian Sub 49008 -

No frequency provided

dupC=0.00000
gnomAD - Exomes American Sub 34588 -

No frequency provided

dupC=0.00009
gnomAD - Exomes African Sub 16256 -

No frequency provided

dupC=0.00000
gnomAD - Exomes Ashkenazi Jewish Sub 10076 -

No frequency provided

dupC=0.00000
gnomAD - Exomes Other Sub 6132 -

No frequency provided

dupC=0.0000
TopMed Global Study-wide 125568 -

No frequency provided

dupC=0.000024
ExAC Global Study-wide 121384 -

No frequency provided

dupC=0.000049
ExAC Europe Sub 73344 -

No frequency provided

dupC=0.00004
ExAC Asian Sub 25154 -

No frequency provided

dupC=0.00000
ExAC American Sub 11576 -

No frequency provided

dupC=0.00026
ExAC African Sub 10402 -

No frequency provided

dupC=0.00000
ExAC Other Sub 908 -

No frequency provided

dupC=0.000
gnomAD - Genomes Global Study-wide 31402 -

No frequency provided

dupC=0.00010
gnomAD - Genomes European Sub 18902 -

No frequency provided

dupC=0.00016
gnomAD - Genomes African Sub 8716 -

No frequency provided

dupC=0.0000
gnomAD - Genomes East Asian Sub 1558 -

No frequency provided

dupC=0.0000
gnomAD - Genomes Other Sub 1088 -

No frequency provided

dupC=0.0000
gnomAD - Genomes American Sub 848 -

No frequency provided

dupC=0.000
gnomAD - Genomes Ashkenazi Jewish Sub 290 -

No frequency provided

dupC=0.000
GO Exome Sequencing Project Global Study-wide 12512 -

No frequency provided

dupC=0.00008
GO Exome Sequencing Project European American Sub 8246 -

No frequency provided

dupC=0.0001
GO Exome Sequencing Project African American Sub 4266 -

No frequency provided

dupC=0.0000
ALFA Total Global 2188 (C)4=0.9995 dupC=0.0005
ALFA European Sub 2072 (C)4=1.0000 dupC=0.0000
ALFA African Sub 82 (C)4=1.00 dupC=0.00
ALFA Other Sub 26 (C)4=0.96 dupC=0.04
ALFA South Asian Sub 4 (C)4=1.0 dupC=0.0
ALFA Asian Sub 4 (C)4=1.0 dupC=0.0
ALFA Latin American 1 Sub 0 (C)4=0 dupC=0
ALFA Latin American 2 Sub 0 (C)4=0 dupC=0
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)4= dupC
GRCh38.p12 chr 3 NC_000003.12:g.120647889_120647892= NC_000003.12:g.120647892dup
GRCh37.p13 chr 3 NC_000003.11:g.120366736_120366739= NC_000003.11:g.120366739dup
HGD RefSeqGene NG_011957.1:g.39590_39593= NG_011957.1:g.39593dup
HGD transcript NM_000187.4:c.454_457= NM_000187.4:c.457dup
HGD transcript NM_000187.3:c.454_457= NM_000187.3:c.457dup
HGD transcript variant X5 XM_005247414.5:c.454_457= XM_005247414.5:c.457dup
HGD transcript variant X3 XM_005247414.1:c.454_457= XM_005247414.1:c.457dup
HGD transcript variant X3 XM_017006277.2:c.31_34= XM_017006277.2:c.34dup
HGD transcript variant X1 XM_005247412.2:c.454_457= XM_005247412.2:c.457dup
HGD transcript variant X1 XM_005247412.1:c.454_457= XM_005247412.1:c.457dup
HGD transcript variant X2 XM_005247413.2:c.454_457= XM_005247413.2:c.457dup
HGD transcript variant X2 XM_005247413.1:c.454_457= XM_005247413.1:c.457dup
HGD transcript variant X4 XM_011512746.2:c.454_457= XM_011512746.2:c.457dup
homogentisate 1,2-dioxygenase NP_000178.2:p.Gly152_Asp153= NP_000178.2:p.Asp153fs
homogentisate 1,2-dioxygenase isoform X5 XP_005247471.1:p.Gly152_Asp153= XP_005247471.1:p.Asp153fs
homogentisate 1,2-dioxygenase isoform X3 XP_016861766.1:p.Gly11_Asp12= XP_016861766.1:p.Asp12fs
homogentisate 1,2-dioxygenase isoform X1 XP_005247469.1:p.Gly152_Asp153= XP_005247469.1:p.Asp153fs
homogentisate 1,2-dioxygenase isoform X2 XP_005247470.1:p.Gly152_Asp153= XP_005247470.1:p.Asp153fs
homogentisate 1,2-dioxygenase isoform X4 XP_011511048.1:p.Gly152_Asp153= XP_011511048.1:p.Asp153fs
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#.

10 SubSNP, 6 Frequency, 1 ClinVar submissions
No Submitter Submission ID Date (Build)
1 OMIM-CURATED-RECORDS ss836188707 Oct 23, 2013 (136)
2 EVA_EXAC ss1711734405 Apr 01, 2015 (144)
3 GNOMAD ss2733990515 Nov 08, 2017 (151)
4 GNOMAD ss2747077599 Nov 08, 2017 (151)
5 GNOMAD ss2798280110 Nov 08, 2017 (151)
6 ILLUMINA ss3022278770 Nov 08, 2017 (151)
7 TOPMED ss3403598843 Nov 08, 2017 (151)
8 ILLUMINA ss3652757293 Oct 12, 2018 (152)
9 ILLUMINA ss3726050089 Jul 13, 2019 (153)
10 EVA ss3823945434 Apr 25, 2020 (154)
11 ExAC NC_000003.11 - 120366736 Oct 12, 2018 (152)
12 gnomAD - Genomes NC_000003.11 - 120366736 Jul 13, 2019 (153)
13 gnomAD - Exomes NC_000003.11 - 120366736 Jul 13, 2019 (153)
14 GO Exome Sequencing Project NC_000003.11 - 120366736 Oct 12, 2018 (152)
15 TopMed NC_000003.12 - 120647889 Oct 12, 2018 (152)
16 dbGaP Population Frequency Project NC_000003.12 - 120647889 Apr 25, 2020 (154)
17 ClinVar RCV000003319.6 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
7094357, 46815631, 3076000, 403739, ss1711734405, ss2733990515, ss2747077599, ss2798280110, ss3022278770, ss3652757293, ss3823945434 NC_000003.11:120366735::C NC_000003.12:120647888:CCCC:CCCCC (self)
261520868, ss836188707, ss3403598843, ss3726050089 NC_000003.12:120647888::C NC_000003.12:120647888:CCCC:CCCCC (self)
RCV000003319.6, 523543173 NC_000003.12:120647888:CCCC:CCCCC NC_000003.12:120647888:CCCC:CCCCC
Removed from this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Destination RSIDs
RCV000003319.5 NC_000003.12:120647888:C:CC NC_000003.12:120647888:CCCC:CCCCC
Help

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

2 citations for rs397515346
PMID Title Author Year Journal
9154114 Molecular defects in alkaptonuria. Gehrig A et al. 1997 Cytogenetics and cell genetics
20301627 Alkaptonuria Introne WJ et al. 1993 GeneReviews®
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