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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.

rs1483991610

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr15:76381540 (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
A>T
Variation Type
SNV Single Nucleotide Variation
Frequency
T=0.000019 (5/264690, TOPMED)
T=0.000007 (1/140272, GnomAD)
T=0.00000 (0/14050, ALFA)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
SCAPER : Synonymous 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 A=1.00000 T=0.00000 1.0 0.0 0.0 N/A
European Sub 9690 A=1.0000 T=0.0000 1.0 0.0 0.0 N/A
African Sub 2898 A=1.0000 T=0.0000 1.0 0.0 0.0 N/A
African Others Sub 114 A=1.000 T=0.000 1.0 0.0 0.0 N/A
African American Sub 2784 A=1.0000 T=0.0000 1.0 0.0 0.0 N/A
Asian Sub 112 A=1.000 T=0.000 1.0 0.0 0.0 N/A
East Asian Sub 86 A=1.00 T=0.00 1.0 0.0 0.0 N/A
Other Asian Sub 26 A=1.00 T=0.00 1.0 0.0 0.0 N/A
Latin American 1 Sub 146 A=1.000 T=0.000 1.0 0.0 0.0 N/A
Latin American 2 Sub 610 A=1.000 T=0.000 1.0 0.0 0.0 N/A
South Asian Sub 98 A=1.00 T=0.00 1.0 0.0 0.0 N/A
Other Sub 496 A=1.000 T=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 A=0.999981 T=0.000019
gnomAD - Genomes Global Study-wide 140272 A=0.999993 T=0.000007
gnomAD - Genomes European Sub 75952 A=1.00000 T=0.00000
gnomAD - Genomes African Sub 42048 A=0.99998 T=0.00002
gnomAD - Genomes American Sub 13662 A=1.00000 T=0.00000
gnomAD - Genomes Ashkenazi Jewish Sub 3322 A=1.0000 T=0.0000
gnomAD - Genomes East Asian Sub 3134 A=1.0000 T=0.0000
gnomAD - Genomes Other Sub 2154 A=1.0000 T=0.0000
Allele Frequency Aggregator Total Global 14050 A=1.00000 T=0.00000
Allele Frequency Aggregator European Sub 9690 A=1.0000 T=0.0000
Allele Frequency Aggregator African Sub 2898 A=1.0000 T=0.0000
Allele Frequency Aggregator Latin American 2 Sub 610 A=1.000 T=0.000
Allele Frequency Aggregator Other Sub 496 A=1.000 T=0.000
Allele Frequency Aggregator Latin American 1 Sub 146 A=1.000 T=0.000
Allele Frequency Aggregator Asian Sub 112 A=1.000 T=0.000
Allele Frequency Aggregator South Asian Sub 98 A=1.00 T=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 15 NC_000015.10:g.76381540A>T
GRCh37.p13 chr 15 NC_000015.9:g.76673881A>T
Gene: SCAPER, S-phase cyclin A associated protein in the ER (minus strand)
Molecule type Change Amino acid[Codon] SO Term
SCAPER transcript variant 1 NM_020843.4:c.3543T>A A [GCT] > A [GCA] Coding Sequence Variant
S phase cyclin A-associated protein in the endoplasmic reticulum isoform a NP_065894.2:p.Ala1181= A (Ala) > A (Ala) Synonymous Variant
SCAPER transcript variant 3 NM_001353009.2:c.3561T>A A [GCT] > A [GCA] Coding Sequence Variant
S phase cyclin A-associated protein in the endoplasmic reticulum isoform c NP_001339938.1:p.Ala1187= A (Ala) > A (Ala) Synonymous Variant
SCAPER transcript variant 7 NM_001353012.2:c.3141T>A A [GCT] > A [GCA] Coding Sequence Variant
S phase cyclin A-associated protein in the endoplasmic reticulum isoform d NP_001339941.1:p.Ala1047= A (Ala) > A (Ala) Synonymous Variant
SCAPER transcript variant 6 NM_001353011.2:c.3159T>A A [GCT] > A [GCA] Coding Sequence Variant
S phase cyclin A-associated protein in the endoplasmic reticulum isoform e NP_001339940.1:p.Ala1053= A (Ala) > A (Ala) Synonymous Variant
SCAPER transcript variant 5 NM_001353010.2:c.3141T>A A [GCT] > A [GCA] Coding Sequence Variant
S phase cyclin A-associated protein in the endoplasmic reticulum isoform d NP_001339939.1:p.Ala1047= A (Ala) > A (Ala) Synonymous Variant
SCAPER transcript variant 2 NM_001145923.2:c.2805T>A A [GCT] > A [GCA] Coding Sequence Variant
S phase cyclin A-associated protein in the endoplasmic reticulum isoform b NP_001139395.1:p.Ala935= A (Ala) > A (Ala) Synonymous Variant
SCAPER transcript variant 4 NR_148227.2:n.3751T>A N/A Non Coding Transcript Variant
SCAPER transcript variant X20 XM_017022283.2:c. N/A Genic Downstream Transcript Variant
SCAPER transcript variant X11 XM_024449940.2:c. N/A Genic Downstream Transcript Variant
SCAPER transcript variant X13 XM_024449941.2:c. N/A Genic Downstream Transcript Variant
SCAPER transcript variant X14 XM_024449942.2:c. N/A Genic Downstream Transcript Variant
SCAPER transcript variant X18 XM_024449944.2:c. N/A Genic Downstream Transcript Variant
SCAPER transcript variant X15 XM_047432628.1:c. N/A Genic Downstream Transcript Variant
SCAPER transcript variant X16 XM_047432629.1:c. N/A Genic Downstream Transcript Variant
SCAPER transcript variant X17 XM_047432630.1:c. N/A Genic Downstream Transcript Variant
SCAPER transcript variant X19 XM_047432631.1:c. N/A Genic Downstream Transcript Variant
SCAPER transcript variant X22 XM_047432632.1:c. N/A Genic Downstream Transcript Variant
SCAPER transcript variant X24 XM_047432634.1:c. N/A Genic Downstream Transcript Variant
SCAPER transcript variant X1 XM_047432620.1:c.3636T>A A [GCT] > A [GCA] Coding Sequence Variant
S phase cyclin A-associated protein in the endoplasmic reticulum isoform X1 XP_047288576.1:p.Ala1212= A (Ala) > A (Ala) Synonymous Variant
SCAPER transcript variant X2 XM_047432621.1:c.3618T>A A [GCT] > A [GCA] Coding Sequence Variant
S phase cyclin A-associated protein in the endoplasmic reticulum isoform X2 XP_047288577.1:p.Ala1206= A (Ala) > A (Ala) Synonymous Variant
SCAPER transcript variant X3 XM_047432622.1:c.3513T>A A [GCT] > A [GCA] Coding Sequence Variant
S phase cyclin A-associated protein in the endoplasmic reticulum isoform X3 XP_047288578.1:p.Ala1171= A (Ala) > A (Ala) Synonymous Variant
SCAPER transcript variant X4 XM_047432623.1:c.3495T>A A [GCT] > A [GCA] Coding Sequence Variant
S phase cyclin A-associated protein in the endoplasmic reticulum isoform X4 XP_047288579.1:p.Ala1165= A (Ala) > A (Ala) Synonymous Variant
SCAPER transcript variant X5 XM_047432624.1:c.3480T>A A [GCT] > A [GCA] Coding Sequence Variant
S phase cyclin A-associated protein in the endoplasmic reticulum isoform X5 XP_047288580.1:p.Ala1160= A (Ala) > A (Ala) Synonymous Variant
SCAPER transcript variant X6 XM_047432625.1:c.3462T>A A [GCT] > A [GCA] Coding Sequence Variant
S phase cyclin A-associated protein in the endoplasmic reticulum isoform X6 XP_047288581.1:p.Ala1154= A (Ala) > A (Ala) Synonymous Variant
SCAPER transcript variant X7 XM_047432626.1:c.3387T>A A [GCT] > A [GCA] Coding Sequence Variant
S phase cyclin A-associated protein in the endoplasmic reticulum isoform X7 XP_047288582.1:p.Ala1129= A (Ala) > A (Ala) Synonymous Variant
SCAPER transcript variant X8 XM_011521653.4:c.3159T>A A [GCT] > A [GCA] Coding Sequence Variant
S phase cyclin A-associated protein in the endoplasmic reticulum isoform X8 XP_011519955.1:p.Ala1053= A (Ala) > A (Ala) Synonymous Variant
SCAPER transcript variant X9 XM_017022273.2:c.3141T>A A [GCT] > A [GCA] Coding Sequence Variant
S phase cyclin A-associated protein in the endoplasmic reticulum isoform X9 XP_016877762.1:p.Ala1047= A (Ala) > A (Ala) Synonymous Variant
SCAPER transcript variant X10 XM_047432627.1:c.2823T>A A [GCT] > A [GCA] Coding Sequence Variant
S phase cyclin A-associated protein in the endoplasmic reticulum isoform X10 XP_047288583.1:p.Ala941= A (Ala) > A (Ala) Synonymous Variant
SCAPER transcript variant X21 XM_011521656.4:c.1701T>A A [GCT] > A [GCA] Coding Sequence Variant
S phase cyclin A-associated protein in the endoplasmic reticulum isoform X20 XP_011519958.1:p.Ala567= A (Ala) > A (Ala) Synonymous Variant
SCAPER transcript variant X23 XM_047432633.1:c.1467T>A A [GCT] > A [GCA] Coding Sequence Variant
S phase cyclin A-associated protein in the endoplasmic reticulum isoform X22 XP_047288589.1:p.Ala489= A (Ala) > A (Ala) Synonymous Variant
SCAPER transcript variant X12 XR_007064448.1:n. N/A Genic Downstream Transcript 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= T
GRCh38.p14 chr 15 NC_000015.10:g.76381540= NC_000015.10:g.76381540A>T
GRCh37.p13 chr 15 NC_000015.9:g.76673881= NC_000015.9:g.76673881A>T
SCAPER transcript variant 1 NM_020843.4:c.3543= NM_020843.4:c.3543T>A
SCAPER transcript variant 1 NM_020843.3:c.3543= NM_020843.3:c.3543T>A
SCAPER transcript variant 1 NM_020843.2:c.3543= NM_020843.2:c.3543T>A
SCAPER transcript variant X8 XM_011521653.4:c.3159= XM_011521653.4:c.3159T>A
SCAPER transcript variant X6 XM_011521653.3:c.3159= XM_011521653.3:c.3159T>A
SCAPER transcript variant X12 XM_011521653.2:c.3159= XM_011521653.2:c.3159T>A
SCAPER transcript variant X8 XM_011521653.1:c.3159= XM_011521653.1:c.3159T>A
SCAPER transcript variant X21 XM_011521656.4:c.1701= XM_011521656.4:c.1701T>A
SCAPER transcript variant X23 XM_011521656.3:c.1701= XM_011521656.3:c.1701T>A
SCAPER transcript variant X27 XM_011521656.2:c.1701= XM_011521656.2:c.1701T>A
SCAPER transcript variant X11 XM_011521656.1:c.1701= XM_011521656.1:c.1701T>A
SCAPER transcript variant 3 NM_001353009.2:c.3561= NM_001353009.2:c.3561T>A
SCAPER transcript variant 3 NM_001353009.1:c.3561= NM_001353009.1:c.3561T>A
SCAPER transcript variant 5 NM_001353010.2:c.3141= NM_001353010.2:c.3141T>A
SCAPER transcript variant 5 NM_001353010.1:c.3141= NM_001353010.1:c.3141T>A
SCAPER transcript variant 6 NM_001353011.2:c.3159= NM_001353011.2:c.3159T>A
SCAPER transcript variant 6 NM_001353011.1:c.3159= NM_001353011.1:c.3159T>A
SCAPER transcript variant 4 NR_148227.2:n.3751= NR_148227.2:n.3751T>A
SCAPER transcript variant 4 NR_148227.1:n.3868= NR_148227.1:n.3868T>A
SCAPER transcript variant 2 NM_001145923.2:c.2805= NM_001145923.2:c.2805T>A
SCAPER transcript variant 2 NM_001145923.1:c.2805= NM_001145923.1:c.2805T>A
SCAPER transcript variant 7 NM_001353012.2:c.3141= NM_001353012.2:c.3141T>A
SCAPER transcript variant 7 NM_001353012.1:c.3141= NM_001353012.1:c.3141T>A
SCAPER transcript variant X9 XM_017022273.2:c.3141= XM_017022273.2:c.3141T>A
SCAPER transcript variant X7 XM_017022273.1:c.3141= XM_017022273.1:c.3141T>A
SCAPER transcript variant X1 XM_047432620.1:c.3636= XM_047432620.1:c.3636T>A
SCAPER transcript variant X2 XM_047432621.1:c.3618= XM_047432621.1:c.3618T>A
SCAPER transcript variant X3 XM_047432622.1:c.3513= XM_047432622.1:c.3513T>A
SCAPER transcript variant X4 XM_047432623.1:c.3495= XM_047432623.1:c.3495T>A
SCAPER transcript variant X5 XM_047432624.1:c.3480= XM_047432624.1:c.3480T>A
SCAPER transcript variant X6 XM_047432625.1:c.3462= XM_047432625.1:c.3462T>A
SCAPER transcript variant X7 XM_047432626.1:c.3387= XM_047432626.1:c.3387T>A
SCAPER transcript variant X10 XM_047432627.1:c.2823= XM_047432627.1:c.2823T>A
SCAPER transcript variant X23 XM_047432633.1:c.1467= XM_047432633.1:c.1467T>A
S phase cyclin A-associated protein in the endoplasmic reticulum isoform a NP_065894.2:p.Ala1181= NP_065894.2:p.Ala1181=
S phase cyclin A-associated protein in the endoplasmic reticulum isoform X8 XP_011519955.1:p.Ala1053= XP_011519955.1:p.Ala1053=
S phase cyclin A-associated protein in the endoplasmic reticulum isoform X20 XP_011519958.1:p.Ala567= XP_011519958.1:p.Ala567=
S phase cyclin A-associated protein in the endoplasmic reticulum isoform c NP_001339938.1:p.Ala1187= NP_001339938.1:p.Ala1187=
S phase cyclin A-associated protein in the endoplasmic reticulum isoform d NP_001339939.1:p.Ala1047= NP_001339939.1:p.Ala1047=
S phase cyclin A-associated protein in the endoplasmic reticulum isoform e NP_001339940.1:p.Ala1053= NP_001339940.1:p.Ala1053=
S phase cyclin A-associated protein in the endoplasmic reticulum isoform b NP_001139395.1:p.Ala935= NP_001139395.1:p.Ala935=
S phase cyclin A-associated protein in the endoplasmic reticulum isoform d NP_001339941.1:p.Ala1047= NP_001339941.1:p.Ala1047=
S phase cyclin A-associated protein in the endoplasmic reticulum isoform X9 XP_016877762.1:p.Ala1047= XP_016877762.1:p.Ala1047=
S phase cyclin A-associated protein in the endoplasmic reticulum isoform X1 XP_047288576.1:p.Ala1212= XP_047288576.1:p.Ala1212=
S phase cyclin A-associated protein in the endoplasmic reticulum isoform X2 XP_047288577.1:p.Ala1206= XP_047288577.1:p.Ala1206=
S phase cyclin A-associated protein in the endoplasmic reticulum isoform X3 XP_047288578.1:p.Ala1171= XP_047288578.1:p.Ala1171=
S phase cyclin A-associated protein in the endoplasmic reticulum isoform X4 XP_047288579.1:p.Ala1165= XP_047288579.1:p.Ala1165=
S phase cyclin A-associated protein in the endoplasmic reticulum isoform X5 XP_047288580.1:p.Ala1160= XP_047288580.1:p.Ala1160=
S phase cyclin A-associated protein in the endoplasmic reticulum isoform X6 XP_047288581.1:p.Ala1154= XP_047288581.1:p.Ala1154=
S phase cyclin A-associated protein in the endoplasmic reticulum isoform X7 XP_047288582.1:p.Ala1129= XP_047288582.1:p.Ala1129=
S phase cyclin A-associated protein in the endoplasmic reticulum isoform X10 XP_047288583.1:p.Ala941= XP_047288583.1:p.Ala941=
S phase cyclin A-associated protein in the endoplasmic reticulum isoform X22 XP_047288589.1:p.Ala489= XP_047288589.1:p.Ala489=
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 ss4291875958 Apr 26, 2021 (155)
2 TOPMED ss4997611066 Apr 26, 2021 (155)
3 gnomAD - Genomes NC_000015.10 - 76381540 Apr 26, 2021 (155)
4 TopMed NC_000015.10 - 76381540 Apr 26, 2021 (155)
5 ALFA NC_000015.10 - 76381540 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
474257021, 213156726, 1099224447, ss4291875958, ss4997611066 NC_000015.10:76381539:A:T NC_000015.10:76381539:A:T (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 rs1483991610

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