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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.

rs555855005

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr8:42541611 (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
C>G
Variation Type
SNV Single Nucleotide Variation
Frequency
G=0.006416 (884/137774, GnomAD)
G=0.00569 (82/14420, ALFA)
G=0.0077 (49/6404, 1000G_30x) (+ 1 more)
G=0.0068 (34/5008, 1000G)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
SLC20A2 : Intron Variant
SMIM19 : Intron Variant
Publications
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: 20230706150541
Population Group Sample Size Ref Allele Alt Allele
Total Global 14420 C=0.99431 G=0.00569
European Sub 9824 C=0.9996 G=0.0004
African Sub 2946 C=0.9759 G=0.0241
African Others Sub 114 C=0.991 G=0.009
African American Sub 2832 C=0.9753 G=0.0247
Asian Sub 112 C=1.000 G=0.000
East Asian Sub 86 C=1.00 G=0.00
Other Asian Sub 26 C=1.00 G=0.00
Latin American 1 Sub 146 C=1.000 G=0.000
Latin American 2 Sub 610 C=0.995 G=0.005
South Asian Sub 98 C=1.00 G=0.00
Other Sub 684 C=0.994 G=0.006


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 - Genomes Global Study-wide 137774 C=0.993584 G=0.006416
gnomAD - Genomes European Sub 74052 C=0.99981 G=0.00019
gnomAD - Genomes African Sub 41720 C=0.98039 G=0.01961
gnomAD - Genomes American Sub 13482 C=0.99711 G=0.00289
gnomAD - Genomes Ashkenazi Jewish Sub 3300 C=1.0000 G=0.0000
gnomAD - Genomes East Asian Sub 3102 C=1.0000 G=0.0000
gnomAD - Genomes Other Sub 2118 C=0.9939 G=0.0061
Allele Frequency Aggregator Total Global 14420 C=0.99431 G=0.00569
Allele Frequency Aggregator European Sub 9824 C=0.9996 G=0.0004
Allele Frequency Aggregator African Sub 2946 C=0.9759 G=0.0241
Allele Frequency Aggregator Other Sub 684 C=0.994 G=0.006
Allele Frequency Aggregator Latin American 2 Sub 610 C=0.995 G=0.005
Allele Frequency Aggregator Latin American 1 Sub 146 C=1.000 G=0.000
Allele Frequency Aggregator Asian Sub 112 C=1.000 G=0.000
Allele Frequency Aggregator South Asian Sub 98 C=1.00 G=0.00
1000Genomes_30x Global Study-wide 6404 C=0.9923 G=0.0077
1000Genomes_30x African Sub 1786 C=0.9726 G=0.0274
1000Genomes_30x Europe Sub 1266 C=1.0000 G=0.0000
1000Genomes_30x South Asian Sub 1202 C=1.0000 G=0.0000
1000Genomes_30x East Asian Sub 1170 C=1.0000 G=0.0000
1000Genomes_30x American Sub 980 C=1.000 G=0.000
1000Genomes Global Study-wide 5008 C=0.9932 G=0.0068
1000Genomes African Sub 1322 C=0.9743 G=0.0257
1000Genomes East Asian Sub 1008 C=1.0000 G=0.0000
1000Genomes Europe Sub 1006 C=1.0000 G=0.0000
1000Genomes South Asian Sub 978 C=1.000 G=0.000
1000Genomes American Sub 694 C=1.000 G=0.000
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 8 NC_000008.11:g.42541611C>G
GRCh37.p13 chr 8 NC_000008.10:g.42396754C>G
SLC20A2 RefSeqGene NG_032161.1:g.5603G>C
Gene: SMIM19, small integral membrane protein 19 (plus strand)
Molecule type Change Amino acid[Codon] SO Term
SMIM19 transcript variant 4 NM_001135676.2:c.-5+412C>G N/A Intron Variant
SMIM19 transcript variant 5 NM_001363186.2:c.-838= N/A 5 Prime UTR Variant
SMIM19 transcript variant 2 NM_001135675.2:c.-549= N/A 5 Prime UTR Variant
SMIM19 transcript variant 1 NM_001135674.2:c.-767= N/A 5 Prime UTR Variant
SMIM19 transcript variant 3 NM_138436.4:c.-99= N/A 5 Prime UTR Variant
Gene: SLC20A2, solute carrier family 20 member 2 (minus strand)
Molecule type Change Amino acid[Codon] SO Term
SLC20A2 transcript variant 2 NM_006749.5:c.-265+210G>C N/A Intron Variant
SLC20A2 transcript variant 1 NM_001257180.2:c. N/A Genic Upstream Transcript Variant
SLC20A2 transcript variant 3 NM_001257181.2:c. N/A Genic Upstream Transcript Variant
SLC20A2 transcript variant X2 XM_017013748.2:c.-265+249…

XM_017013748.2:c.-265+249G>C

N/A Intron Variant
SLC20A2 transcript variant X12 XM_024447237.2:c.-265+249…

XM_024447237.2:c.-265+249G>C

N/A Intron Variant
SLC20A2 transcript variant X1 XM_005273613.4:c.-338= N/A 5 Prime UTR Variant
SLC20A2 transcript variant X3 XM_024447235.2:c.-961= N/A 5 Prime UTR Variant
SLC20A2 transcript variant X6 XM_047422121.1:c.-1099= N/A 5 Prime UTR Variant
SLC20A2 transcript variant X8 XM_006716390.5:c.-338= N/A 5 Prime UTR Variant
SLC20A2 transcript variant X9 XM_017013749.3:c. N/A Genic Upstream Transcript Variant
SLC20A2 transcript variant X13 XM_017013752.3:c. N/A Genic Upstream Transcript Variant
SLC20A2 transcript variant X4 XM_024447236.2:c. N/A Genic Upstream Transcript Variant
SLC20A2 transcript variant X5 XM_047422120.1:c. N/A Genic Upstream Transcript Variant
SLC20A2 transcript variant X7 XM_047422122.1:c. N/A Genic Upstream Transcript Variant
SLC20A2 transcript variant X10 XM_047422123.1:c. N/A Genic Upstream Transcript Variant
SLC20A2 transcript variant X11 XM_047422124.1:c. N/A Genic Upstream 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.

Not Reported in ClinVar
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= G
GRCh38.p14 chr 8 NC_000008.11:g.42541611= NC_000008.11:g.42541611C>G
GRCh37.p13 chr 8 NC_000008.10:g.42396754= NC_000008.10:g.42396754C>G
SLC20A2 RefSeqGene NG_032161.1:g.5603= NG_032161.1:g.5603G>C
SLC20A2 transcript variant X8 XM_006716390.5:c.-338= XM_006716390.5:c.-338G>C
SLC20A2 transcript variant X7 XM_006716390.4:c.-338= XM_006716390.4:c.-338G>C
SLC20A2 transcript variant X5 XM_006716390.3:c.-338= XM_006716390.3:c.-338G>C
SLC20A2 transcript variant X3 XM_006716390.2:c.-338= XM_006716390.2:c.-338G>C
SLC20A2 transcript variant X4 XM_006716390.1:c.-338= XM_006716390.1:c.-338G>C
SLC20A2 transcript variant X1 XM_005273613.4:c.-338= XM_005273613.4:c.-338G>C
SLC20A2 transcript variant X1 XM_005273613.3:c.-338= XM_005273613.3:c.-338G>C
SLC20A2 transcript variant X1 XM_005273613.2:c.-338= XM_005273613.2:c.-338G>C
SLC20A2 transcript variant X1 XM_005273613.1:c.-338= XM_005273613.1:c.-338G>C
SMIM19 transcript variant 3 NM_138436.4:c.-99= NM_138436.4:c.-99C>G
SMIM19 transcript variant 3 NM_138436.3:c.-99= NM_138436.3:c.-99C>G
SLC20A2 transcript variant X3 XM_024447235.2:c.-961= XM_024447235.2:c.-961G>C
SMIM19 transcript variant 5 NM_001363186.2:c.-838= NM_001363186.2:c.-838C>G
SMIM19 transcript variant 1 NM_001135674.2:c.-767= NM_001135674.2:c.-767C>G
SMIM19 transcript variant 2 NM_001135675.2:c.-549= NM_001135675.2:c.-549C>G
SLC20A2 transcript variant X6 XM_047422121.1:c.-1099= XM_047422121.1:c.-1099G>C
SMIM19 transcript variant 4 NM_001135676.1:c.-5+412= NM_001135676.1:c.-5+412C>G
SMIM19 transcript variant 4 NM_001135676.2:c.-5+412= NM_001135676.2:c.-5+412C>G
SLC20A2 transcript variant 2 NM_006749.4:c.-265+210= NM_006749.4:c.-265+210G>C
SLC20A2 transcript variant 2 NM_006749.5:c.-265+210= NM_006749.5:c.-265+210G>C
SLC20A2 transcript variant X2 XM_005273614.1:c.-265+249= XM_005273614.1:c.-265+249G>C
SLC20A2 transcript variant X2 XM_017013748.2:c.-265+249= XM_017013748.2:c.-265+249G>C
SLC20A2 transcript variant X12 XM_024447237.2:c.-265+249= XM_024447237.2:c.-265+249G>C
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#.

9 SubSNP, 4 Frequency submissions
No Submitter Submission ID Date (Build)
1 1000GENOMES ss1329579773 Aug 21, 2014 (142)
2 GNOMAD ss2865972957 Nov 08, 2017 (151)
3 KHV_HUMAN_GENOMES ss3811081460 Jul 13, 2019 (153)
4 1000G_HIGH_COVERAGE ss5276908110 Oct 16, 2022 (156)
5 EVA ss5380718678 Oct 16, 2022 (156)
6 HUGCELL_USP ss5473507679 Oct 16, 2022 (156)
7 EVA ss5509329086 Oct 16, 2022 (156)
8 1000G_HIGH_COVERAGE ss5567128464 Oct 16, 2022 (156)
9 EVA ss5888696478 Oct 16, 2022 (156)
10 1000Genomes NC_000008.10 - 42396754 Oct 12, 2018 (152)
11 1000Genomes_30x NC_000008.11 - 42541611 Oct 16, 2022 (156)
12 gnomAD - Genomes NC_000008.11 - 42541611 Apr 26, 2021 (155)
13 ALFA NC_000008.11 - 42541611 Apr 26, 2021 (155)
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
41696551, ss1329579773, ss2865972957, ss5380718678, ss5509329086 NC_000008.10:42396753:C:G NC_000008.11:42541610:C:G (self)
54654399, 294004496, 8303542426, ss3811081460, ss5276908110, ss5473507679, ss5567128464, ss5888696478 NC_000008.11:42541610:C:G NC_000008.11:42541610:C:G (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 rs555855005

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