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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.

rs1459941410

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr13:28713200 (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
Variation Type
Deletion
Frequency
delA=0.000004 (1/251158, GnomAD_exome)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
SLC46A3 : Frameshift Variant
Publications
0 citations
Genomic View
See rs on genome
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 251158 A=0.999996 delA=0.000004
gnomAD - Exomes European Sub 135182 A=0.999993 delA=0.000007
gnomAD - Exomes Asian Sub 48996 A=1.00000 delA=0.00000
gnomAD - Exomes American Sub 34560 A=1.00000 delA=0.00000
gnomAD - Exomes African Sub 16218 A=1.00000 delA=0.00000
gnomAD - Exomes Ashkenazi Jewish Sub 10076 A=1.00000 delA=0.00000
gnomAD - Exomes Other Sub 6126 A=1.0000 delA=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 13 NC_000013.11:g.28713200del
GRCh37.p13 chr 13 NC_000013.10:g.29287337del
SLC46A3 RefSeqGene NG_053189.1:g.10814del
Gene: SLC46A3, solute carrier family 46 member 3 (minus strand)
Molecule type Change Amino acid[Codon] SO Term
SLC46A3 transcript variant 2 NM_001135919.2:c.540del T [ACT] > T [AC] Coding Sequence Variant
lysosomal proton-coupled steroid conjugate and bile acid symporter SLC46A3 isoform b precursor NP_001129391.1:p.Gly181fs T (Thr) > T (Thr) Frameshift Variant
SLC46A3 transcript variant 1 NM_181785.4:c.540del T [ACT] > T [AC] Coding Sequence Variant
lysosomal proton-coupled steroid conjugate and bile acid symporter SLC46A3 isoform a precursor NP_861450.1:p.Gly181fs T (Thr) > T (Thr) Frameshift Variant
SLC46A3 transcript variant 3 NM_001347960.2:c.540del T [ACT] > T [AC] Coding Sequence Variant
lysosomal proton-coupled steroid conjugate and bile acid symporter SLC46A3 isoform a precursor NP_001334889.1:p.Gly181fs T (Thr) > T (Thr) Frameshift Variant
SLC46A3 transcript variant X1 XM_005266361.3:c.540del T [ACT] > T [AC] Coding Sequence Variant
lysosomal proton-coupled steroid conjugate and bile acid symporter SLC46A3 isoform X1 XP_005266418.1:p.Gly181fs T (Thr) > T (Thr) 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 A= delA
GRCh38.p14 chr 13 NC_000013.11:g.28713200= NC_000013.11:g.28713200del
GRCh37.p13 chr 13 NC_000013.10:g.29287337= NC_000013.10:g.29287337del
SLC46A3 RefSeqGene NG_053189.1:g.10814= NG_053189.1:g.10814del
SLC46A3 transcript variant 1 NM_181785.4:c.540= NM_181785.4:c.540del
SLC46A3 transcript variant 1 NM_181785.3:c.540= NM_181785.3:c.540del
SLC46A3 transcript variant 3 NM_001347960.2:c.540= NM_001347960.2:c.540del
SLC46A3 transcript variant 3 NM_001347960.1:c.540= NM_001347960.1:c.540del
SLC46A3 transcript variant 2 NM_001135919.2:c.540= NM_001135919.2:c.540del
SLC46A3 transcript variant 2 NM_001135919.1:c.540= NM_001135919.1:c.540del
SLC46A3 transcript variant X1 XM_005266361.3:c.540= XM_005266361.3:c.540del
SLC46A3 transcript variant X1 XM_005266361.2:c.540= XM_005266361.2:c.540del
SLC46A3 transcript variant X1 XM_005266361.1:c.540= XM_005266361.1:c.540del
lysosomal proton-coupled steroid conjugate and bile acid symporter SLC46A3 isoform a precursor NP_861450.1:p.Thr180= NP_861450.1:p.Gly181fs
lysosomal proton-coupled steroid conjugate and bile acid symporter SLC46A3 isoform a precursor NP_001334889.1:p.Thr180= NP_001334889.1:p.Gly181fs
lysosomal proton-coupled steroid conjugate and bile acid symporter SLC46A3 isoform b precursor NP_001129391.1:p.Thr180= NP_001129391.1:p.Gly181fs
lysosomal proton-coupled steroid conjugate and bile acid symporter SLC46A3 isoform X1 XP_005266418.1:p.Thr180= XP_005266418.1:p.Gly181fs
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, 1 Frequency submissions
No Submitter Submission ID Date (Build)
1 GNOMAD ss2740339794 Nov 08, 2017 (151)
2 gnomAD - Exomes NC_000013.10 - 29287337 Jul 13, 2019 (153)
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
9581882, ss2740339794 NC_000013.10:29287336:A: NC_000013.11:28713199:A: (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 rs1459941410

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