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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.

rs397515528

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr10:125812222 (GRCh38.p14) 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
G>A
Variation Type
SNV Single Nucleotide Variation
Frequency
A=0.000 (0/476, ALFA)
Clinical Significance
Reported in ClinVar
Gene : Consequence
UROS : Missense Variant
Publications
1 citation
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: 20230706150541
Population Group Sample Size Ref Allele Alt Allele
Total Global 476 G=1.000 A=0.000
European Sub 0 G=0 A=0
African Sub 424 G=1.000 A=0.000
African Others Sub 0 G=0 A=0
African American Sub 424 G=1.000 A=0.000
Asian Sub 0 G=0 A=0
East Asian Sub 0 G=0 A=0
Other Asian Sub 0 G=0 A=0
Latin American 1 Sub 0 G=0 A=0
Latin American 2 Sub 0 G=0 A=0
South Asian Sub 0 G=0 A=0
Other Sub 52 G=1.00 A=0.00


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
Allele Frequency Aggregator Total Global 476 G=1.000 A=0.000
Allele Frequency Aggregator African Sub 424 G=1.000 A=0.000
Allele Frequency Aggregator Other Sub 52 G=1.00 A=0.00
Allele Frequency Aggregator European Sub 0 G=0 A=0
Allele Frequency Aggregator Latin American 1 Sub 0 G=0 A=0
Allele Frequency Aggregator Latin American 2 Sub 0 G=0 A=0
Allele Frequency Aggregator South Asian Sub 0 G=0 A=0
Allele Frequency Aggregator Asian Sub 0 G=0 A=0
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.p14 chr 10 NC_000010.11:g.125812222G>A
GRCh37.p13 chr 10 NC_000010.10:g.127500791G>A
UROS RefSeqGene (LRG_1081) NG_011557.2:g.16047C>T
Gene: UROS, uroporphyrinogen III synthase (minus strand)
Molecule type Change Amino acid[Codon] SO Term
UROS transcript variant 2 NM_000375.3:c.311C>T A [GCT] > V [GTT] Coding Sequence Variant
uroporphyrinogen-III synthase isoform 2 NP_000366.1:p.Ala104Val A (Ala) > V (Val) Missense Variant
UROS transcript variant 3 NM_001324037.2:c.311C>T A [GCT] > V [GTT] Coding Sequence Variant
uroporphyrinogen-III synthase isoform 3 NP_001310966.1:p.Ala104Val A (Ala) > V (Val) Missense Variant
UROS transcript variant 1 NM_001324036.2:c.311C>T A [GCT] > V [GTT] Coding Sequence Variant
uroporphyrinogen-III synthase isoform 1 NP_001310965.1:p.Ala104Val A (Ala) > V (Val) Missense Variant
UROS transcript variant 4 NM_001324038.2:c.311C>T A [GCT] > V [GTT] Coding Sequence Variant
uroporphyrinogen-III synthase isoform 4 NP_001310967.1:p.Ala104Val A (Ala) > V (Val) Missense Variant
UROS transcript variant 5 NM_001324039.2:c.311C>T A [GCT] > V [GTT] Coding Sequence Variant
uroporphyrinogen-III synthase isoform 5 NP_001310968.1:p.Ala104Val A (Ala) > V (Val) Missense Variant
UROS transcript variant 9 NR_136678.2:n.297C>T N/A Non Coding Transcript Variant
UROS transcript variant 7 NR_136676.2:n.567C>T N/A Non Coding Transcript Variant
UROS transcript variant 6 NR_136675.2:n.386C>T N/A Non Coding Transcript Variant
UROS transcript variant 8 NR_136677.2:n.567C>T N/A Non Coding Transcript Variant
UROS transcript variant X1 XM_017016611.3:c.311C>T A [GCT] > V [GTT] Coding Sequence Variant
uroporphyrinogen-III synthase isoform X1 XP_016872100.2:p.Ala104Val A (Ala) > V (Val) Missense Variant
UROS transcript variant X2 XM_024448154.2:c.311C>T A [GCT] > V [GTT] Coding Sequence Variant
uroporphyrinogen-III synthase isoform X2 XP_024303922.1:p.Ala104Val A (Ala) > V (Val) Missense Variant
UROS transcript variant X3 XM_047425708.1:c.311C>T A [GCT] > V [GTT] Coding Sequence Variant
uroporphyrinogen-III synthase isoform X3 XP_047281664.1:p.Ala104Val A (Ala) > V (Val) Missense Variant
UROS transcript variant X4 XM_017016612.3:c.311C>T A [GCT] > V [GTT] Coding Sequence Variant
uroporphyrinogen-III synthase isoform X4 XP_016872101.1:p.Ala104Val A (Ala) > V (Val) Missense Variant
UROS transcript variant X5 XM_011540127.3:c.311C>T A [GCT] > V [GTT] Coding Sequence Variant
uroporphyrinogen-III synthase isoform X5 XP_011538429.1:p.Ala104Val A (Ala) > V (Val) Missense Variant
UROS transcript variant X6 XM_005270140.6:c.311C>T A [GCT] > V [GTT] Coding Sequence Variant
uroporphyrinogen-III synthase isoform X6 XP_005270197.1:p.Ala104Val A (Ala) > V (Val) Missense Variant
UROS transcript variant X8 XM_047425709.1:c.311C>T A [GCT] > V [GTT] Coding Sequence Variant
uroporphyrinogen-III synthase isoform X6 XP_047281665.1:p.Ala104Val A (Ala) > V (Val) Missense Variant
UROS transcript variant X10 XM_024448155.2:c.311C>T A [GCT] > V [GTT] Coding Sequence Variant
uroporphyrinogen-III synthase isoform X7 XP_024303923.1:p.Ala104Val A (Ala) > V (Val) Missense Variant
UROS transcript variant X11 XM_047425710.1:c.311C>T A [GCT] > V [GTT] Coding Sequence Variant
uroporphyrinogen-III synthase isoform X8 XP_047281666.1:p.Ala104Val A (Ala) > V (Val) Missense Variant
UROS transcript variant X13 XM_047425711.1:c.311C>T A [GCT] > V [GTT] Coding Sequence Variant
uroporphyrinogen-III synthase isoform X9 XP_047281667.1:p.Ala104Val A (Ala) > V (Val) Missense Variant
UROS transcript variant X7 XR_001747196.3:n.567C>T N/A Non Coding Transcript Variant
UROS transcript variant X9 XR_007061985.1:n.567C>T N/A Non Coding Transcript Variant
UROS transcript variant X12 XR_007061986.1:n.567C>T N/A Non Coding Transcript 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: A (allele ID: 76509 )
ClinVar Accession Disease Names Clinical Significance
RCV000055809.3 Cutaneous porphyria Pathogenic
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 G= A
GRCh38.p14 chr 10 NC_000010.11:g.125812222= NC_000010.11:g.125812222G>A
GRCh37.p13 chr 10 NC_000010.10:g.127500791= NC_000010.10:g.127500791G>A
UROS RefSeqGene (LRG_1081) NG_011557.2:g.16047= NG_011557.2:g.16047C>T
UROS transcript variant 2 NM_000375.3:c.311= NM_000375.3:c.311C>T
UROS transcript variant 2 NM_000375.2:c.311= NM_000375.2:c.311C>T
UROS transcript variant 5 NM_001324039.2:c.311= NM_001324039.2:c.311C>T
UROS transcript variant 5 NM_001324039.1:c.311= NM_001324039.1:c.311C>T
UROS transcript variant 7 NR_136676.2:n.567= NR_136676.2:n.567C>T
UROS transcript variant 7 NR_136676.1:n.577= NR_136676.1:n.577C>T
UROS transcript variant 1 NM_001324036.2:c.311= NM_001324036.2:c.311C>T
UROS transcript variant 1 NM_001324036.1:c.311= NM_001324036.1:c.311C>T
UROS transcript variant 8 NR_136677.2:n.567= NR_136677.2:n.567C>T
UROS transcript variant 8 NR_136677.1:n.577= NR_136677.1:n.577C>T
UROS transcript variant 3 NM_001324037.2:c.311= NM_001324037.2:c.311C>T
UROS transcript variant 3 NM_001324037.1:c.311= NM_001324037.1:c.311C>T
UROS transcript variant 4 NM_001324038.2:c.311= NM_001324038.2:c.311C>T
UROS transcript variant 4 NM_001324038.1:c.311= NM_001324038.1:c.311C>T
UROS transcript variant 6 NR_136675.2:n.386= NR_136675.2:n.386C>T
UROS transcript variant 6 NR_136675.1:n.396= NR_136675.1:n.396C>T
UROS transcript variant 9 NR_136678.2:n.297= NR_136678.2:n.297C>T
UROS transcript variant 9 NR_136678.1:n.307= NR_136678.1:n.307C>T
UROS transcript variant X6 XM_005270140.6:c.311= XM_005270140.6:c.311C>T
UROS transcript variant X5 XM_005270140.5:c.311= XM_005270140.5:c.311C>T
UROS transcript variant X5 XM_005270140.4:c.311= XM_005270140.4:c.311C>T
UROS transcript variant X7 XM_005270140.3:c.311= XM_005270140.3:c.311C>T
UROS transcript variant X4 XM_005270140.2:c.311= XM_005270140.2:c.311C>T
UROS transcript variant X4 XM_005270140.1:c.311= XM_005270140.1:c.311C>T
UROS transcript variant X7 XR_001747196.3:n.567= XR_001747196.3:n.567C>T
UROS transcript variant X6 XR_001747196.2:n.434= XR_001747196.2:n.434C>T
UROS transcript variant X6 XR_001747196.1:n.419= XR_001747196.1:n.419C>T
UROS transcript variant X1 XM_017016611.3:c.311= XM_017016611.3:c.311C>T
UROS transcript variant X1 XM_017016611.2:c.311= XM_017016611.2:c.311C>T
UROS transcript variant X2 XM_017016611.1:c.311= XM_017016611.1:c.311C>T
UROS transcript variant X4 XM_017016612.3:c.311= XM_017016612.3:c.311C>T
UROS transcript variant X3 XM_017016612.2:c.311= XM_017016612.2:c.311C>T
UROS transcript variant X3 XM_017016612.1:c.311= XM_017016612.1:c.311C>T
UROS transcript variant X5 XM_011540127.3:c.311= XM_011540127.3:c.311C>T
UROS transcript variant X4 XM_011540127.2:c.311= XM_011540127.2:c.311C>T
UROS transcript variant X4 XM_011540127.1:c.311= XM_011540127.1:c.311C>T
UROS transcript variant X10 XM_024448155.2:c.311= XM_024448155.2:c.311C>T
UROS transcript variant X8 XM_024448155.1:c.311= XM_024448155.1:c.311C>T
UROS transcript variant X2 XM_024448154.2:c.311= XM_024448154.2:c.311C>T
UROS transcript variant X2 XM_024448154.1:c.311= XM_024448154.1:c.311C>T
UROS transcript variant X9 XR_007061985.1:n.567= XR_007061985.1:n.567C>T
UROS transcript variant X8 XM_047425709.1:c.311= XM_047425709.1:c.311C>T
UROS transcript variant X11 XM_047425710.1:c.311= XM_047425710.1:c.311C>T
UROS transcript variant X13 XM_047425711.1:c.311= XM_047425711.1:c.311C>T
UROS transcript variant X3 XM_047425708.1:c.311= XM_047425708.1:c.311C>T
UROS transcript variant X12 XR_007061986.1:n.567= XR_007061986.1:n.567C>T
uroporphyrinogen-III synthase isoform 2 NP_000366.1:p.Ala104= NP_000366.1:p.Ala104Val
uroporphyrinogen-III synthase isoform 5 NP_001310968.1:p.Ala104= NP_001310968.1:p.Ala104Val
uroporphyrinogen-III synthase isoform 1 NP_001310965.1:p.Ala104= NP_001310965.1:p.Ala104Val
uroporphyrinogen-III synthase isoform 3 NP_001310966.1:p.Ala104= NP_001310966.1:p.Ala104Val
uroporphyrinogen-III synthase isoform 4 NP_001310967.1:p.Ala104= NP_001310967.1:p.Ala104Val
uroporphyrinogen-III synthase isoform X6 XP_005270197.1:p.Ala104= XP_005270197.1:p.Ala104Val
uroporphyrinogen-III synthase isoform X1 XP_016872100.2:p.Ala104= XP_016872100.2:p.Ala104Val
uroporphyrinogen-III synthase isoform X4 XP_016872101.1:p.Ala104= XP_016872101.1:p.Ala104Val
uroporphyrinogen-III synthase isoform X5 XP_011538429.1:p.Ala104= XP_011538429.1:p.Ala104Val
uroporphyrinogen-III synthase isoform X7 XP_024303923.1:p.Ala104= XP_024303923.1:p.Ala104Val
uroporphyrinogen-III synthase isoform X2 XP_024303922.1:p.Ala104= XP_024303922.1:p.Ala104Val
uroporphyrinogen-III synthase isoform X6 XP_047281665.1:p.Ala104= XP_047281665.1:p.Ala104Val
uroporphyrinogen-III synthase isoform X8 XP_047281666.1:p.Ala104= XP_047281666.1:p.Ala104Val
uroporphyrinogen-III synthase isoform X9 XP_047281667.1:p.Ala104= XP_047281667.1:p.Ala104Val
uroporphyrinogen-III synthase isoform X3 XP_047281664.1:p.Ala104= XP_047281664.1:p.Ala104Val
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#.

2 SubSNP, 1 Frequency, 1 ClinVar submissions
No Submitter Submission ID Date (Build)
1 CLINVAR ss836189098 Oct 23, 2013 (136)
2 ILLUMINA ss3725199068 Jul 13, 2019 (153)
3 ALFA NC_000010.11 - 125812222 Apr 26, 2021 (155)
4 ClinVar RCV000055809.3 Oct 16, 2022 (156)
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
RCV000055809.3, 2089805033, ss836189098, ss3725199068 NC_000010.11:125812221:G:A NC_000010.11:125812221:G:A (self)
Help

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

1 citation for rs397515528
PMID Title Author Year Journal
24027798 Congenital Erythropoietic Porphyria. Erwin A 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.post761+d5e8e07