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dbSNP Short Genetic Variations

Examples: rs268, BRCA1 and more Advanced search

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.

rs1474548313

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr22:32237260-32237263 (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
delA / dupA
Variation Type
Indel Insertion and Deletion
Frequency
delA=0.000004 (1/243858, GnomAD_exome)
dupA=0.00002 (1/65434, ALFA)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
SLC5A4 : Frameshift Variant
SLC5A4-AS1 : 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: 20231103111315
Population Group Sample Size Ref Allele Alt Allele Ref HMOZ Alt HMOZ HTRZ HWEP
Total Global 65434 AAAA=0.99998 AAAAA=0.00002 0.999969 0.0 3.1e-05 0
European Sub 59704 AAAA=0.99998 AAAAA=0.00002 0.999967 0.0 0.000033 0
African Sub 800 AAAA=1.000 AAAAA=0.000 1.0 0.0 0.0 N/A
African Others Sub 52 AAAA=1.00 AAAAA=0.00 1.0 0.0 0.0 N/A
African American Sub 748 AAAA=1.000 AAAAA=0.000 1.0 0.0 0.0 N/A
Asian Sub 3162 AAAA=1.0000 AAAAA=0.0000 1.0 0.0 0.0 N/A
East Asian Sub 2562 AAAA=1.0000 AAAAA=0.0000 1.0 0.0 0.0 N/A
Other Asian Sub 600 AAAA=1.000 AAAAA=0.000 1.0 0.0 0.0 N/A
Latin American 1 Sub 290 AAAA=1.000 AAAAA=0.000 1.0 0.0 0.0 N/A
Latin American 2 Sub 318 AAAA=1.000 AAAAA=0.000 1.0 0.0 0.0 N/A
South Asian Sub 176 AAAA=1.000 AAAAA=0.000 1.0 0.0 0.0 N/A
Other Sub 984 AAAA=1.000 AAAAA=0.000 1.0 0.0 0.0 N/A


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 243858 (A)4=0.999996 delA=0.000004
gnomAD - Exomes European Sub 130980 (A)4=0.999992 delA=0.000008
gnomAD - Exomes Asian Sub 47678 (A)4=1.00000 delA=0.00000
gnomAD - Exomes American Sub 34022 (A)4=1.00000 delA=0.00000
gnomAD - Exomes African Sub 15300 (A)4=1.00000 delA=0.00000
gnomAD - Exomes Ashkenazi Jewish Sub 9868 (A)4=1.0000 delA=0.0000
gnomAD - Exomes Other Sub 6010 (A)4=1.0000 delA=0.0000
Allele Frequency Aggregator Total Global 65434 (A)4=0.99998 dupA=0.00002
Allele Frequency Aggregator European Sub 59704 (A)4=0.99998 dupA=0.00002
Allele Frequency Aggregator Asian Sub 3162 (A)4=1.0000 dupA=0.0000
Allele Frequency Aggregator Other Sub 984 (A)4=1.000 dupA=0.000
Allele Frequency Aggregator African Sub 800 (A)4=1.000 dupA=0.000
Allele Frequency Aggregator Latin American 2 Sub 318 (A)4=1.000 dupA=0.000
Allele Frequency Aggregator Latin American 1 Sub 290 (A)4=1.000 dupA=0.000
Allele Frequency Aggregator South Asian Sub 176 (A)4=1.000 dupA=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 22 NC_000022.11:g.32237263del
GRCh38.p14 chr 22 NC_000022.11:g.32237263dup
GRCh37.p13 chr 22 NC_000022.10:g.32633250del
GRCh37.p13 chr 22 NC_000022.10:g.32633250dup
Gene: SLC5A4, solute carrier family 5 member 4 (minus strand)
Molecule type Change Amino acid[Codon] SO Term
SLC5A4 transcript NM_014227.3:c.648del F [TTT] > L [TT] Coding Sequence Variant
probable glucose sensor protein SLC5A4 NP_055042.1:p.Phe216fs F (Phe) > L (Leu) Frameshift Variant
SLC5A4 transcript NM_014227.3:c.648dup I [ATT] > Y [TATT] Coding Sequence Variant
probable glucose sensor protein SLC5A4 NP_055042.1:p.Ile217fs I (Ile) > Y (Tyr) Frameshift Variant
SLC5A4 transcript variant X1 XM_017028920.2:c.738del F [TTT] > L [TT] Coding Sequence Variant
probable glucose sensor protein SLC5A4 isoform X1 XP_016884409.1:p.Phe246fs F (Phe) > L (Leu) Frameshift Variant
SLC5A4 transcript variant X1 XM_017028920.2:c.738dup I [ATT] > Y [TATT] Coding Sequence Variant
probable glucose sensor protein SLC5A4 isoform X1 XP_016884409.1:p.Ile247fs I (Ile) > Y (Tyr) Frameshift Variant
SLC5A4 transcript variant X2 XM_011530342.3:c.510del F [TTT] > L [TT] Coding Sequence Variant
probable glucose sensor protein SLC5A4 isoform X2 XP_011528644.1:p.Phe170fs F (Phe) > L (Leu) Frameshift Variant
SLC5A4 transcript variant X2 XM_011530342.3:c.510dup I [ATT] > Y [TATT] Coding Sequence Variant
probable glucose sensor protein SLC5A4 isoform X2 XP_011528644.1:p.Ile171fs I (Ile) > Y (Tyr) Frameshift Variant
SLC5A4 transcript variant X3 XM_006724308.4:c.510del F [TTT] > L [TT] Coding Sequence Variant
probable glucose sensor protein SLC5A4 isoform X2 XP_006724371.1:p.Phe170fs F (Phe) > L (Leu) Frameshift Variant
SLC5A4 transcript variant X3 XM_006724308.4:c.510dup I [ATT] > Y [TATT] Coding Sequence Variant
probable glucose sensor protein SLC5A4 isoform X2 XP_006724371.1:p.Ile171fs I (Ile) > Y (Tyr) Frameshift Variant
SLC5A4 transcript variant X4 XM_011530343.3:c.510del F [TTT] > L [TT] Coding Sequence Variant
probable glucose sensor protein SLC5A4 isoform X2 XP_011528645.1:p.Phe170fs F (Phe) > L (Leu) Frameshift Variant
SLC5A4 transcript variant X4 XM_011530343.3:c.510dup I [ATT] > Y [TATT] Coding Sequence Variant
probable glucose sensor protein SLC5A4 isoform X2 XP_011528645.1:p.Ile171fs I (Ile) > Y (Tyr) Frameshift Variant
SLC5A4 transcript variant X5 XM_011530344.3:c.441del F [TTT] > L [TT] Coding Sequence Variant
probable glucose sensor protein SLC5A4 isoform X3 XP_011528646.1:p.Phe147fs F (Phe) > L (Leu) Frameshift Variant
SLC5A4 transcript variant X5 XM_011530344.3:c.441dup I [ATT] > Y [TATT] Coding Sequence Variant
probable glucose sensor protein SLC5A4 isoform X3 XP_011528646.1:p.Ile148fs I (Ile) > Y (Tyr) Frameshift Variant
Gene: SLC5A4-AS1, SLC5A4 antisense RNA 1 (plus strand)
Molecule type Change Amino acid[Codon] SO Term
SLC5A4-AS1 transcript NR_149072.1:n. N/A Intron 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 (A)4= delA dupA
GRCh38.p14 chr 22 NC_000022.11:g.32237260_32237263= NC_000022.11:g.32237263del NC_000022.11:g.32237263dup
GRCh37.p13 chr 22 NC_000022.10:g.32633247_32633250= NC_000022.10:g.32633250del NC_000022.10:g.32633250dup
SLC5A4 transcript variant X3 XM_006724308.4:c.507_510= XM_006724308.4:c.510del XM_006724308.4:c.510dup
SLC5A4 transcript variant X3 XM_006724308.3:c.507_510= XM_006724308.3:c.510del XM_006724308.3:c.510dup
SLC5A4 transcript variant X2 XM_006724308.2:c.507_510= XM_006724308.2:c.510del XM_006724308.2:c.510dup
SLC5A4 transcript variant X1 XM_006724308.1:c.507_510= XM_006724308.1:c.510del XM_006724308.1:c.510dup
SLC5A4 transcript variant X2 XM_011530342.3:c.507_510= XM_011530342.3:c.510del XM_011530342.3:c.510dup
SLC5A4 transcript variant X2 XM_011530342.2:c.507_510= XM_011530342.2:c.510del XM_011530342.2:c.510dup
SLC5A4 transcript variant X1 XM_011530342.1:c.507_510= XM_011530342.1:c.510del XM_011530342.1:c.510dup
SLC5A4 transcript variant X5 XM_011530344.3:c.438_441= XM_011530344.3:c.441del XM_011530344.3:c.441dup
SLC5A4 transcript variant X5 XM_011530344.2:c.438_441= XM_011530344.2:c.441del XM_011530344.2:c.441dup
SLC5A4 transcript variant X4 XM_011530344.1:c.438_441= XM_011530344.1:c.441del XM_011530344.1:c.441dup
SLC5A4 transcript NM_014227.3:c.645_648= NM_014227.3:c.648del NM_014227.3:c.648dup
SLC5A4 transcript NM_014227.2:c.645_648= NM_014227.2:c.648del NM_014227.2:c.648dup
SLC5A4 transcript variant X4 XM_011530343.3:c.507_510= XM_011530343.3:c.510del XM_011530343.3:c.510dup
SLC5A4 transcript variant X4 XM_011530343.2:c.507_510= XM_011530343.2:c.510del XM_011530343.2:c.510dup
SLC5A4 transcript variant X3 XM_011530343.1:c.507_510= XM_011530343.1:c.510del XM_011530343.1:c.510dup
SLC5A4 transcript variant X1 XM_017028920.2:c.735_738= XM_017028920.2:c.738del XM_017028920.2:c.738dup
SLC5A4 transcript variant X1 XM_017028920.1:c.735_738= XM_017028920.1:c.738del XM_017028920.1:c.738dup
probable glucose sensor protein SLC5A4 isoform X2 XP_006724371.1:p.Ser169_Phe170= XP_006724371.1:p.Phe170fs XP_006724371.1:p.Ile171fs
probable glucose sensor protein SLC5A4 isoform X2 XP_011528644.1:p.Ser169_Phe170= XP_011528644.1:p.Phe170fs XP_011528644.1:p.Ile171fs
probable glucose sensor protein SLC5A4 isoform X3 XP_011528646.1:p.Ser146_Phe147= XP_011528646.1:p.Phe147fs XP_011528646.1:p.Ile148fs
probable glucose sensor protein SLC5A4 NP_055042.1:p.Ser215_Phe216= NP_055042.1:p.Phe216fs NP_055042.1:p.Ile217fs
probable glucose sensor protein SLC5A4 isoform X2 XP_011528645.1:p.Ser169_Phe170= XP_011528645.1:p.Phe170fs XP_011528645.1:p.Ile171fs
probable glucose sensor protein SLC5A4 isoform X1 XP_016884409.1:p.Ser245_Phe246= XP_016884409.1:p.Phe246fs XP_016884409.1:p.Ile247fs
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#.

1 SubSNP, 2 Frequency submissions
No Submitter Submission ID Date (Build)
1 GNOMAD ss2745097791 Nov 08, 2017 (151)
2 gnomAD - Exomes NC_000022.10 - 32633247 Jul 13, 2019 (153)
3 ALFA NC_000022.11 - 32237260 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
14428594, ss2745097791 NC_000022.10:32633246:A: NC_000022.11:32237259:AAAA:AAA (self)
11112360465 NC_000022.11:32237259:AAAA:AAAAA NC_000022.11:32237259:AAAA:AAAAA (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 rs1474548313

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.post820+afb47a3d