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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.

rs765043342

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr17:7283256-7283260 (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
delCCTC
Variation Type
Indel Insertion and Deletion
Frequency
delCCTC=0.000038 (10/264690, TOPMED)
delCCTC=0.000008 (2/251490, GnomAD_exome)
delCCTC=0.000064 (9/140240, GnomAD) (+ 2 more)
delCCTC=0.000016 (2/121412, ExAC)
delCCTC=0.00000 (0/10680, ALFA)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
SLC2A4 : Frameshift 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 CCCTC=1.00000 C=0.00000
European Sub 6962 CCCTC=1.0000 C=0.0000
African Sub 2294 CCCTC=1.0000 C=0.0000
African Others Sub 84 CCCTC=1.00 C=0.00
African American Sub 2210 CCCTC=1.0000 C=0.0000
Asian Sub 108 CCCTC=1.000 C=0.000
East Asian Sub 84 CCCTC=1.00 C=0.00
Other Asian Sub 24 CCCTC=1.00 C=0.00
Latin American 1 Sub 146 CCCTC=1.000 C=0.000
Latin American 2 Sub 610 CCCTC=1.000 C=0.000
South Asian Sub 94 CCCTC=1.00 C=0.00
Other Sub 466 CCCTC=1.000 C=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 CCCTC=0.999962 delCCTC=0.000038
gnomAD - Exomes Global Study-wide 251490 CCCTC=0.999992 delCCTC=0.000008
gnomAD - Exomes European Sub 135414 CCCTC=0.999993 delCCTC=0.000007
gnomAD - Exomes Asian Sub 49010 CCCTC=1.00000 delCCTC=0.00000
gnomAD - Exomes American Sub 34592 CCCTC=0.99997 delCCTC=0.00003
gnomAD - Exomes African Sub 16256 CCCTC=1.00000 delCCTC=0.00000
gnomAD - Exomes Ashkenazi Jewish Sub 10078 CCCTC=1.00000 delCCTC=0.00000
gnomAD - Exomes Other Sub 6140 CCCTC=1.0000 delCCTC=0.0000
gnomAD - Genomes Global Study-wide 140240 CCCTC=0.999936 delCCTC=0.000064
gnomAD - Genomes European Sub 75954 CCCTC=0.99999 delCCTC=0.00001
gnomAD - Genomes African Sub 42030 CCCTC=1.00000 delCCTC=0.00000
gnomAD - Genomes American Sub 13652 CCCTC=0.99941 delCCTC=0.00059
gnomAD - Genomes Ashkenazi Jewish Sub 3324 CCCTC=1.0000 delCCTC=0.0000
gnomAD - Genomes East Asian Sub 3128 CCCTC=1.0000 delCCTC=0.0000
gnomAD - Genomes Other Sub 2152 CCCTC=1.0000 delCCTC=0.0000
ExAC Global Study-wide 121412 CCCTC=0.999984 delCCTC=0.000016
ExAC Europe Sub 73354 CCCTC=0.99999 delCCTC=0.00001
ExAC Asian Sub 25166 CCCTC=1.00000 delCCTC=0.00000
ExAC American Sub 11578 CCCTC=0.99991 delCCTC=0.00009
ExAC African Sub 10406 CCCTC=1.00000 delCCTC=0.00000
ExAC Other Sub 908 CCCTC=1.000 delCCTC=0.000
Allele Frequency Aggregator Total Global 10680 CCCTC=1.00000 delCCTC=0.00000
Allele Frequency Aggregator European Sub 6962 CCCTC=1.0000 delCCTC=0.0000
Allele Frequency Aggregator African Sub 2294 CCCTC=1.0000 delCCTC=0.0000
Allele Frequency Aggregator Latin American 2 Sub 610 CCCTC=1.000 delCCTC=0.000
Allele Frequency Aggregator Other Sub 466 CCCTC=1.000 delCCTC=0.000
Allele Frequency Aggregator Latin American 1 Sub 146 CCCTC=1.000 delCCTC=0.000
Allele Frequency Aggregator Asian Sub 108 CCCTC=1.000 delCCTC=0.000
Allele Frequency Aggregator South Asian Sub 94 CCCTC=1.00 delCCTC=0.00
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 17 NC_000017.11:g.7283257_7283260del
GRCh37.p13 chr 17 NC_000017.10:g.7186576_7186579del
SLC2A4 RefSeqGene NG_012127.1:g.6523_6526del
GRCh38.p14 chr 17 fix patch HG2087_PATCH NW_021160020.1:g.38585_38588del
Gene: SLC2A4, solute carrier family 2 member 4 (plus strand)
Molecule type Change Amino acid[Codon] SO Term
SLC2A4 transcript NM_001042.3:c.46_49del P [CCT] > S [AG] Coding Sequence Variant
solute carrier family 2, facilitated glucose transporter member 4 NP_001033.1:p.Pro16fs P (Pro) > S (Ser) 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.

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 CCCTC= delCCTC
GRCh38.p14 chr 17 NC_000017.11:g.7283256_7283260= NC_000017.11:g.7283257_7283260del
GRCh37.p13 chr 17 NC_000017.10:g.7186575_7186579= NC_000017.10:g.7186576_7186579del
SLC2A4 RefSeqGene NG_012127.1:g.6522_6526= NG_012127.1:g.6523_6526del
SLC2A4 transcript NM_001042.3:c.45_49= NM_001042.3:c.46_49del
SLC2A4 transcript NM_001042.2:c.45_49= NM_001042.2:c.46_49del
GRCh38.p14 chr 17 fix patch HG2087_PATCH NW_021160020.1:g.38584_38588= NW_021160020.1:g.38585_38588del
solute carrier family 2, facilitated glucose transporter member 4 NP_001033.1:p.Pro15_Gln17= NP_001033.1:p.Pro16fs
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#.

5 SubSNP, 5 Frequency submissions
No Submitter Submission ID Date (Build)
1 EVA_EXAC ss1712128756 Apr 01, 2015 (144)
2 GNOMAD ss2742389538 Nov 08, 2017 (151)
3 GNOMAD ss2749673740 Nov 08, 2017 (151)
4 GNOMAD ss2947401290 Nov 08, 2017 (151)
5 TOPMED ss5028567707 Apr 27, 2021 (155)
6 ExAC NC_000017.10 - 7186575 Oct 12, 2018 (152)
7 gnomAD - Genomes NC_000017.11 - 7283256 Apr 27, 2021 (155)
8 gnomAD - Exomes NC_000017.10 - 7186575 Jul 13, 2019 (153)
9 TopMed NC_000017.11 - 7283256 Apr 27, 2021 (155)
10 ALFA NC_000017.11 - 7283256 Apr 27, 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
2993025, 11687228, ss1712128756, ss2742389538, ss2749673740, ss2947401290 NC_000017.10:7186574:CCCT: NC_000017.11:7283255:CCCTC:C (self)
500730527, 244113369, ss5028567707 NC_000017.11:7283255:CCCT: NC_000017.11:7283255:CCCTC:C (self)
12215004181 NC_000017.11:7283255:CCCTC:C NC_000017.11:7283255:CCCTC:C (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 rs765043342

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