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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.

rs772611258

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr8:42417565-42417570 (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
delCAC
Variation Type
Indel Insertion and Deletion
Frequency
delCAC=0.000004 (1/264690, TOPMED)
delCAC=0.00000 (0/10680, ALFA)
delCAC=0.0000 (0/3854, ALSPAC) (+ 1 more)
delCAC=0.0003 (1/3708, TWINSUK)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
SLC20A2 : 3 Prime UTR 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 10680 CACCAC=1.00000 CAC=0.00000
European Sub 6962 CACCAC=1.0000 CAC=0.0000
African Sub 2294 CACCAC=1.0000 CAC=0.0000
African Others Sub 84 CACCAC=1.00 CAC=0.00
African American Sub 2210 CACCAC=1.0000 CAC=0.0000
Asian Sub 108 CACCAC=1.000 CAC=0.000
East Asian Sub 84 CACCAC=1.00 CAC=0.00
Other Asian Sub 24 CACCAC=1.00 CAC=0.00
Latin American 1 Sub 146 CACCAC=1.000 CAC=0.000
Latin American 2 Sub 610 CACCAC=1.000 CAC=0.000
South Asian Sub 94 CACCAC=1.00 CAC=0.00
Other Sub 466 CACCAC=1.000 CAC=0.000


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
TopMed Global Study-wide 264690 (CAC)2=0.999996 delCAC=0.000004
Allele Frequency Aggregator Total Global 10680 (CAC)2=1.00000 delCAC=0.00000
Allele Frequency Aggregator European Sub 6962 (CAC)2=1.0000 delCAC=0.0000
Allele Frequency Aggregator African Sub 2294 (CAC)2=1.0000 delCAC=0.0000
Allele Frequency Aggregator Latin American 2 Sub 610 (CAC)2=1.000 delCAC=0.000
Allele Frequency Aggregator Other Sub 466 (CAC)2=1.000 delCAC=0.000
Allele Frequency Aggregator Latin American 1 Sub 146 (CAC)2=1.000 delCAC=0.000
Allele Frequency Aggregator Asian Sub 108 (CAC)2=1.000 delCAC=0.000
Allele Frequency Aggregator South Asian Sub 94 (CAC)2=1.00 delCAC=0.00
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 (CAC)2=1.0000 delCAC=0.0000
UK 10K study - Twins TWIN COHORT Study-wide 3708 (CAC)2=0.9997 delCAC=0.0003
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.42417565CAC[1]
GRCh37.p13 chr 8 NC_000008.10:g.42275083CAC[1]
SLC20A2 RefSeqGene NG_032161.1:g.127269GTG[1]
Gene: SLC20A2, solute carrier family 20 member 2 (minus strand)
Molecule type Change Amino acid[Codon] SO Term
SLC20A2 transcript variant 1 NM_001257180.2:c.*233_*23…

NM_001257180.2:c.*233_*238=

N/A 3 Prime UTR Variant
SLC20A2 transcript variant 2 NM_006749.5:c.*233_*238= N/A 3 Prime UTR Variant
SLC20A2 transcript variant 3 NM_001257181.2:c.*233_*23…

NM_001257181.2:c.*233_*238=

N/A 3 Prime UTR Variant
SLC20A2 transcript variant X1 XM_005273613.4:c.*233_*23…

XM_005273613.4:c.*233_*238=

N/A 3 Prime UTR Variant
SLC20A2 transcript variant X2 XM_017013748.2:c.*233_*23…

XM_017013748.2:c.*233_*238=

N/A 3 Prime UTR Variant
SLC20A2 transcript variant X3 XM_024447235.2:c.*233_*23…

XM_024447235.2:c.*233_*238=

N/A 3 Prime UTR Variant
SLC20A2 transcript variant X4 XM_024447236.2:c.*233_*23…

XM_024447236.2:c.*233_*238=

N/A 3 Prime UTR Variant
SLC20A2 transcript variant X5 XM_047422120.1:c.*233_*23…

XM_047422120.1:c.*233_*238=

N/A 3 Prime UTR Variant
SLC20A2 transcript variant X6 XM_047422121.1:c.*233_*23…

XM_047422121.1:c.*233_*238=

N/A 3 Prime UTR Variant
SLC20A2 transcript variant X7 XM_047422122.1:c.*233_*23…

XM_047422122.1:c.*233_*238=

N/A 3 Prime UTR Variant
SLC20A2 transcript variant X8 XM_006716390.5:c.*233_*23…

XM_006716390.5:c.*233_*238=

N/A 3 Prime UTR Variant
SLC20A2 transcript variant X9 XM_017013749.3:c.*233_*23…

XM_017013749.3:c.*233_*238=

N/A 3 Prime UTR Variant
SLC20A2 transcript variant X10 XM_047422123.1:c.*233_*23…

XM_047422123.1:c.*233_*238=

N/A 3 Prime UTR Variant
SLC20A2 transcript variant X11 XM_047422124.1:c.*233_*23…

XM_047422124.1:c.*233_*238=

N/A 3 Prime UTR Variant
SLC20A2 transcript variant X12 XM_024447237.2:c.*233_*23…

XM_024447237.2:c.*233_*238=

N/A 3 Prime UTR Variant
SLC20A2 transcript variant X13 XM_017013752.3:c.*233_*23…

XM_017013752.3:c.*233_*238=

N/A 3 Prime UTR 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 (CAC)2= delCAC
GRCh38.p14 chr 8 NC_000008.11:g.42417565_42417570= NC_000008.11:g.42417565CAC[1]
GRCh37.p13 chr 8 NC_000008.10:g.42275083_42275088= NC_000008.10:g.42275083CAC[1]
SLC20A2 RefSeqGene NG_032161.1:g.127269_127274= NG_032161.1:g.127269GTG[1]
SLC20A2 transcript variant 2 NM_006749.5:c.*233_*238= NM_006749.5:c.*233GTG[1]
SLC20A2 transcript variant 2 NM_006749.4:c.*233_*238= NM_006749.4:c.*233GTG[1]
SLC20A2 transcript variant 1 NM_001257180.2:c.*233_*238= NM_001257180.2:c.*233GTG[1]
SLC20A2 transcript variant 1 NM_001257180.1:c.*233_*238= NM_001257180.1:c.*233GTG[1]
SLC20A2 transcript variant 3 NM_001257181.2:c.*233_*238= NM_001257181.2:c.*233GTG[1]
SLC20A2 transcript variant 3 NM_001257181.1:c.*233_*238= NM_001257181.1:c.*233GTG[1]
SLC20A2 transcript variant X8 XM_006716390.5:c.*233_*238= XM_006716390.5:c.*233GTG[1]
SLC20A2 transcript variant X7 XM_006716390.4:c.*233_*238= XM_006716390.4:c.*233GTG[1]
SLC20A2 transcript variant X5 XM_006716390.3:c.*233_*238= XM_006716390.3:c.*233GTG[1]
SLC20A2 transcript variant X3 XM_006716390.2:c.*233_*238= XM_006716390.2:c.*233GTG[1]
SLC20A2 transcript variant X4 XM_006716390.1:c.*233_*238= XM_006716390.1:c.*233GTG[1]
SLC20A2 transcript variant X1 XM_005273613.4:c.*233_*238= XM_005273613.4:c.*233GTG[1]
SLC20A2 transcript variant X1 XM_005273613.3:c.*233_*238= XM_005273613.3:c.*233GTG[1]
SLC20A2 transcript variant X1 XM_005273613.2:c.*233_*238= XM_005273613.2:c.*233GTG[1]
SLC20A2 transcript variant X1 XM_005273613.1:c.*233_*238= XM_005273613.1:c.*233GTG[1]
SLC20A2 transcript variant X13 XM_017013752.3:c.*233_*238= XM_017013752.3:c.*233GTG[1]
SLC20A2 transcript variant X12 XM_017013752.2:c.*233_*238= XM_017013752.2:c.*233GTG[1]
SLC20A2 transcript variant X9 XM_017013752.1:c.*233_*238= XM_017013752.1:c.*233GTG[1]
SLC20A2 transcript variant X9 XM_017013749.3:c.*233_*238= XM_017013749.3:c.*233GTG[1]
SLC20A2 transcript variant X6 XM_017013749.2:c.*233_*238= XM_017013749.2:c.*233GTG[1]
SLC20A2 transcript variant X4 XM_017013749.1:c.*233_*238= XM_017013749.1:c.*233GTG[1]
SLC20A2 transcript variant X3 XM_024447235.2:c.*233_*238= XM_024447235.2:c.*233GTG[1]
SLC20A2 transcript variant X2 XM_024447235.1:c.*233_*238= XM_024447235.1:c.*233GTG[1]
SLC20A2 transcript variant X4 XM_024447236.2:c.*233_*238= XM_024447236.2:c.*233GTG[1]
SLC20A2 transcript variant X4 XM_024447236.1:c.*233_*238= XM_024447236.1:c.*233GTG[1]
SLC20A2 transcript variant X2 XM_017013748.2:c.*233_*238= XM_017013748.2:c.*233GTG[1]
SLC20A2 transcript variant X3 XM_017013748.1:c.*233_*238= XM_017013748.1:c.*233GTG[1]
SLC20A2 transcript variant X12 XM_024447237.2:c.*233_*238= XM_024447237.2:c.*233GTG[1]
SLC20A2 transcript variant X8 XM_024447237.1:c.*233_*238= XM_024447237.1:c.*233GTG[1]
SLC20A2 transcript variant X10 XM_047422123.1:c.*233_*238= XM_047422123.1:c.*233GTG[1]
SLC20A2 transcript variant X6 XM_047422121.1:c.*233_*238= XM_047422121.1:c.*233GTG[1]
SLC20A2 transcript variant X5 XM_047422120.1:c.*233_*238= XM_047422120.1:c.*233GTG[1]
SLC20A2 transcript variant X7 XM_047422122.1:c.*233_*238= XM_047422122.1:c.*233GTG[1]
SLC20A2 transcript variant X11 XM_047422124.1:c.*233_*238= XM_047422124.1:c.*233GTG[1]
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#.

3 SubSNP, 4 Frequency submissions
No Submitter Submission ID Date (Build)
1 EVA_UK10K_ALSPAC ss1706032076 Apr 01, 2015 (144)
2 EVA_UK10K_TWINSUK ss1706032087 Apr 01, 2015 (144)
3 TOPMED ss4783724909 Apr 26, 2021 (155)
4 The Avon Longitudinal Study of Parents and Children NC_000008.10 - 42275083 Oct 12, 2018 (152)
5 TopMed NC_000008.11 - 42417565 Apr 26, 2021 (155)
6 UK 10K study - Twins NC_000008.10 - 42275083 Oct 12, 2018 (152)
7 ALFA NC_000008.11 - 42417565 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
23187441, 23187441, ss1706032076, ss1706032087 NC_000008.10:42275082:CAC: NC_000008.11:42417564:CACCAC:CAC (self)
621102469, ss4783724909 NC_000008.11:42417564:CAC: NC_000008.11:42417564:CACCAC:CAC (self)
813945583 NC_000008.11:42417564:CACCAC:CAC NC_000008.11:42417564:CACCAC:CAC (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 rs772611258

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