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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.

rs1491140104

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr11:62210854-62210859 (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
delCA
Variation Type
Indel Insertion and Deletion
Frequency
delCA=0.000004 (1/264690, TOPMED)
delCA=0.000014 (2/139582, GnomAD)
delCA=0.00000 (0/14050, ALFA) (+ 2 more)
delCA=0.0003 (1/3854, ALSPAC)
delCA=0.0000 (0/3708, TWINSUK)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
SCGB2A1 : 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 14050 CACACA=1.00000 CACA=0.00000 1.0 0.0 0.0 N/A
European Sub 9690 CACACA=1.0000 CACA=0.0000 1.0 0.0 0.0 N/A
African Sub 2898 CACACA=1.0000 CACA=0.0000 1.0 0.0 0.0 N/A
African Others Sub 114 CACACA=1.000 CACA=0.000 1.0 0.0 0.0 N/A
African American Sub 2784 CACACA=1.0000 CACA=0.0000 1.0 0.0 0.0 N/A
Asian Sub 112 CACACA=1.000 CACA=0.000 1.0 0.0 0.0 N/A
East Asian Sub 86 CACACA=1.00 CACA=0.00 1.0 0.0 0.0 N/A
Other Asian Sub 26 CACACA=1.00 CACA=0.00 1.0 0.0 0.0 N/A
Latin American 1 Sub 146 CACACA=1.000 CACA=0.000 1.0 0.0 0.0 N/A
Latin American 2 Sub 610 CACACA=1.000 CACA=0.000 1.0 0.0 0.0 N/A
South Asian Sub 98 CACACA=1.00 CACA=0.00 1.0 0.0 0.0 N/A
Other Sub 496 CACACA=1.000 CACA=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
TopMed Global Study-wide 264690 (CA)3=0.999996 delCA=0.000004
gnomAD - Genomes Global Study-wide 139582 (CA)3=0.999986 delCA=0.000014
gnomAD - Genomes European Sub 75608 (CA)3=0.99999 delCA=0.00001
gnomAD - Genomes African Sub 41800 (CA)3=1.00000 delCA=0.00000
gnomAD - Genomes American Sub 13582 (CA)3=0.99993 delCA=0.00007
gnomAD - Genomes Ashkenazi Jewish Sub 3320 (CA)3=1.0000 delCA=0.0000
gnomAD - Genomes East Asian Sub 3126 (CA)3=1.0000 delCA=0.0000
gnomAD - Genomes Other Sub 2146 (CA)3=1.0000 delCA=0.0000
Allele Frequency Aggregator Total Global 14050 (CA)3=1.00000 delCA=0.00000
Allele Frequency Aggregator European Sub 9690 (CA)3=1.0000 delCA=0.0000
Allele Frequency Aggregator African Sub 2898 (CA)3=1.0000 delCA=0.0000
Allele Frequency Aggregator Latin American 2 Sub 610 (CA)3=1.000 delCA=0.000
Allele Frequency Aggregator Other Sub 496 (CA)3=1.000 delCA=0.000
Allele Frequency Aggregator Latin American 1 Sub 146 (CA)3=1.000 delCA=0.000
Allele Frequency Aggregator Asian Sub 112 (CA)3=1.000 delCA=0.000
Allele Frequency Aggregator South Asian Sub 98 (CA)3=1.00 delCA=0.00
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 (CA)3=0.9997 delCA=0.0003
UK 10K study - Twins TWIN COHORT Study-wide 3708 (CA)3=1.0000 delCA=0.0000
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 11 NC_000011.10:g.62210854CA[2]
GRCh37.p13 chr 11 NC_000011.9:g.61978326CA[2]
Gene: SCGB2A1, secretoglobin family 2A member 1 (plus strand)
Molecule type Change Amino acid[Codon] SO Term
SCGB2A1 transcript NM_002407.3:c.243+254CA[2] 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 (CA)3= delCA
GRCh38.p14 chr 11 NC_000011.10:g.62210854_62210859= NC_000011.10:g.62210854CA[2]
GRCh37.p13 chr 11 NC_000011.9:g.61978326_61978331= NC_000011.9:g.61978326CA[2]
SCGB2A1 transcript NM_002407.2:c.243+254= NM_002407.2:c.243+254CA[2]
SCGB2A1 transcript NM_002407.3:c.243+254= NM_002407.3:c.243+254CA[2]
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#.

4 SubSNP, 5 Frequency submissions
No Submitter Submission ID Date (Build)
1 EVA_UK10K_ALSPAC ss1707126187 Jan 10, 2018 (151)
2 EVA_UK10K_TWINSUK ss1707126188 Jan 10, 2018 (151)
3 GNOMAD ss4236201026 Apr 26, 2021 (155)
4 TOPMED ss4887520834 Apr 26, 2021 (155)
5 The Avon Longitudinal Study of Parents and Children NC_000011.9 - 61978326 Oct 12, 2018 (152)
6 gnomAD - Genomes NC_000011.10 - 62210854 Apr 26, 2021 (155)
7 TopMed NC_000011.10 - 62210854 Apr 26, 2021 (155)
8 UK 10K study - Twins NC_000011.9 - 61978326 Oct 12, 2018 (152)
9 ALFA NC_000011.10 - 62210854 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
30024681, 30024681, ss1707126187, ss1707126188 NC_000011.9:61978325:CA: NC_000011.10:62210853:CACACA:CACA (self)
381613355, 103066490, ss4236201026, ss4887520834 NC_000011.10:62210853:CA: NC_000011.10:62210853:CACACA:CACA (self)
7304939704 NC_000011.10:62210853:CACACA:CACA NC_000011.10:62210853:CACACA:CACA (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 rs1491140104

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