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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.

rs1491033503

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr19:49519488-49519492 (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
delC / dupC
Variation Type
Indel Insertion and Deletion
Frequency
dupC=0.000008 (2/264690, TOPMED)
dupC=0.000007 (1/140222, GnomAD)
delC=0.00000 (0/10680, ALFA) (+ 1 more)
dupC=0.00000 (0/10680, ALFA)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
FCGRT : 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 10680 CCCCC=1.00000 CCCC=0.00000, CCCCCC=0.00000 1.0 0.0 0.0 N/A
European Sub 6962 CCCCC=1.0000 CCCC=0.0000, CCCCCC=0.0000 1.0 0.0 0.0 N/A
African Sub 2294 CCCCC=1.0000 CCCC=0.0000, CCCCCC=0.0000 1.0 0.0 0.0 N/A
African Others Sub 84 CCCCC=1.00 CCCC=0.00, CCCCCC=0.00 1.0 0.0 0.0 N/A
African American Sub 2210 CCCCC=1.0000 CCCC=0.0000, CCCCCC=0.0000 1.0 0.0 0.0 N/A
Asian Sub 108 CCCCC=1.000 CCCC=0.000, CCCCCC=0.000 1.0 0.0 0.0 N/A
East Asian Sub 84 CCCCC=1.00 CCCC=0.00, CCCCCC=0.00 1.0 0.0 0.0 N/A
Other Asian Sub 24 CCCCC=1.00 CCCC=0.00, CCCCCC=0.00 1.0 0.0 0.0 N/A
Latin American 1 Sub 146 CCCCC=1.000 CCCC=0.000, CCCCCC=0.000 1.0 0.0 0.0 N/A
Latin American 2 Sub 610 CCCCC=1.000 CCCC=0.000, CCCCCC=0.000 1.0 0.0 0.0 N/A
South Asian Sub 94 CCCCC=1.00 CCCC=0.00, CCCCCC=0.00 1.0 0.0 0.0 N/A
Other Sub 466 CCCCC=1.000 CCCC=0.000, CCCCCC=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 -

No frequency provided

dupC=0.000008
gnomAD - Genomes Global Study-wide 140222 -

No frequency provided

dupC=0.000007
gnomAD - Genomes European Sub 75960 -

No frequency provided

dupC=0.00000
gnomAD - Genomes African Sub 42036 -

No frequency provided

dupC=0.00000
gnomAD - Genomes American Sub 13616 -

No frequency provided

dupC=0.00007
gnomAD - Genomes Ashkenazi Jewish Sub 3324 -

No frequency provided

dupC=0.0000
gnomAD - Genomes East Asian Sub 3132 -

No frequency provided

dupC=0.0000
gnomAD - Genomes Other Sub 2154 -

No frequency provided

dupC=0.0000
Allele Frequency Aggregator Total Global 10680 (C)5=1.00000 delC=0.00000, dupC=0.00000
Allele Frequency Aggregator European Sub 6962 (C)5=1.0000 delC=0.0000, dupC=0.0000
Allele Frequency Aggregator African Sub 2294 (C)5=1.0000 delC=0.0000, dupC=0.0000
Allele Frequency Aggregator Latin American 2 Sub 610 (C)5=1.000 delC=0.000, dupC=0.000
Allele Frequency Aggregator Other Sub 466 (C)5=1.000 delC=0.000, dupC=0.000
Allele Frequency Aggregator Latin American 1 Sub 146 (C)5=1.000 delC=0.000, dupC=0.000
Allele Frequency Aggregator Asian Sub 108 (C)5=1.000 delC=0.000, dupC=0.000
Allele Frequency Aggregator South Asian Sub 94 (C)5=1.00 delC=0.00, dupC=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 19 NC_000019.10:g.49519492del
GRCh38.p14 chr 19 NC_000019.10:g.49519492dup
GRCh37.p13 chr 19 NC_000019.9:g.50022749del
GRCh37.p13 chr 19 NC_000019.9:g.50022749dup
Gene: FCGRT, Fc gamma receptor and transporter (plus strand)
Molecule type Change Amino acid[Codon] SO Term
FCGRT transcript variant 1 NM_001136019.3:c.601+5006…

NM_001136019.3:c.601+5006del

N/A Intron Variant
FCGRT transcript variant 2 NM_004107.5:c.601+5006del N/A Intron Variant
FCGRT transcript variant X1 XM_047438408.1:c.688-2203…

XM_047438408.1:c.688-2203del

N/A Intron Variant
FCGRT transcript variant X2 XM_047438409.1:c.326-5015…

XM_047438409.1:c.326-5015del

N/A Intron Variant
FCGRT transcript variant X2 XM_047438410.1:c.687+3293…

XM_047438410.1:c.687+3293del

N/A Intron Variant
FCGRT transcript variant X3 XM_047438411.1:c.181+5006…

XM_047438411.1:c.181+5006del

N/A Intron Variant
FCGRT transcript variant X4 XM_047438412.1:c.602-2203…

XM_047438412.1:c.602-2203del

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 (C)5= delC dupC
GRCh38.p14 chr 19 NC_000019.10:g.49519488_49519492= NC_000019.10:g.49519492del NC_000019.10:g.49519492dup
GRCh37.p13 chr 19 NC_000019.9:g.50022745_50022749= NC_000019.9:g.50022749del NC_000019.9:g.50022749dup
FCGRT transcript variant 1 NM_001136019.2:c.601+5002= NM_001136019.2:c.601+5006del NM_001136019.2:c.601+5006dup
FCGRT transcript variant 1 NM_001136019.3:c.601+5002= NM_001136019.3:c.601+5006del NM_001136019.3:c.601+5006dup
FCGRT transcript variant 2 NM_004107.4:c.601+5002= NM_004107.4:c.601+5006del NM_004107.4:c.601+5006dup
FCGRT transcript variant 2 NM_004107.5:c.601+5002= NM_004107.5:c.601+5006del NM_004107.5:c.601+5006dup
FCGRT transcript variant X1 XM_005258656.1:c.326-5019= XM_005258656.1:c.326-5015del XM_005258656.1:c.326-5015dup
FCGRT transcript variant X3 XM_005258657.1:c.181+5002= XM_005258657.1:c.181+5006del XM_005258657.1:c.181+5006dup
FCGRT transcript variant X1 XM_047438408.1:c.688-2207= XM_047438408.1:c.688-2203del XM_047438408.1:c.688-2203dup
FCGRT transcript variant X2 XM_047438409.1:c.326-5019= XM_047438409.1:c.326-5015del XM_047438409.1:c.326-5015dup
FCGRT transcript variant X2 XM_047438410.1:c.687+3289= XM_047438410.1:c.687+3293del XM_047438410.1:c.687+3293dup
FCGRT transcript variant X3 XM_047438411.1:c.181+5002= XM_047438411.1:c.181+5006del XM_047438411.1:c.181+5006dup
FCGRT transcript variant X4 XM_047438412.1:c.602-2207= XM_047438412.1:c.602-2203del XM_047438412.1:c.602-2203dup
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#.

2 SubSNP, 3 Frequency submissions
No Submitter Submission ID Date (Build)
1 GNOMAD ss2963752115 Nov 17, 2017 (151)
2 TOPMED ss5077349072 Apr 27, 2021 (155)
3 gnomAD - Genomes NC_000019.10 - 49519488 Apr 27, 2021 (155)
4 TopMed NC_000019.10 - 49519488 Apr 27, 2021 (155)
5 ALFA NC_000019.10 - 49519488 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
7230861153 NC_000019.10:49519487:CCCCC:CCCC NC_000019.10:49519487:CCCCC:CCCC (self)
ss2963752115 NC_000019.9:50022744::C NC_000019.10:49519487:CCCCC:CCCCCC (self)
542246019, 292894736, ss5077349072 NC_000019.10:49519487::C NC_000019.10:49519487:CCCCC:CCCCCC (self)
7230861153 NC_000019.10:49519487:CCCCC:CCCCCC NC_000019.10:49519487:CCCCC:CCCCCC (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 rs1491033503

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