Name: rs1491554377
Published: September 21, 2022
License: Open Access

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.

rs1491554377

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr5:151458312-151458313 (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: dupGT / insGTGT / ins(GT)₃
Variation Type: Indel Insertion and Deletion
Frequency: dupGT=0.00000 (0/11862, ALFA)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: SLC36A1 : 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	HWEP
Total	Global	11862	GT=1.00000	GTGT=0.00000	1.0	N/A
European	Sub	7618	GT=1.0000	GTGT=0.0000	1.0	N/A
African	Sub	2816	GT=1.0000	GTGT=0.0000	1.0	N/A
African Others	Sub	108	GT=1.000	GTGT=0.000	1.0	N/A
African American	Sub	2708	GT=1.0000	GTGT=0.0000	1.0	N/A
Asian	Sub	108	GT=1.000	GTGT=0.000	1.0	N/A
East Asian	Sub	84	GT=1.00	GTGT=0.00	1.0	N/A
Other Asian	Sub	24	GT=1.00	GTGT=0.00	1.0	N/A
Latin American 1	Sub	146	GT=1.000	GTGT=0.000	1.0	N/A
Latin American 2	Sub	610	GT=1.000	GTGT=0.000	1.0	N/A
South Asian	Sub	94	GT=1.00	GTGT=0.00	1.0	N/A
Other	Sub	470	GT=1.000	GTGT=0.000	1.0	N/A

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").

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Study	Population	Group	Sample Size	Ref Allele	Alt Allele
Allele Frequency Aggregator	Total	Global	11862	GT=1.00000	dupGT=0.00000
Allele Frequency Aggregator	European	Sub	7618	GT=1.0000	dupGT=0.0000
Allele Frequency Aggregator	African	Sub	2816	GT=1.0000	dupGT=0.0000
Allele Frequency Aggregator	Latin American 2	Sub	610	GT=1.000	dupGT=0.000
Allele Frequency Aggregator	Other	Sub	470	GT=1.000	dupGT=0.000
Allele Frequency Aggregator	Latin American 1	Sub	146	GT=1.000	dupGT=0.000
Allele Frequency Aggregator	Asian	Sub	108	GT=1.000	dupGT=0.000
Allele Frequency Aggregator	South Asian	Sub	94	GT=1.00	dupGT=0.00

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 5	NC_000005.10:g.151458312_151458313dup
GRCh38.p14 chr 5	NC_000005.10:g.151458312GT[3]
GRCh38.p14 chr 5	NC_000005.10:g.151458312GT[4]
GRCh37.p13 chr 5	NC_000005.9:g.150837873_150837874dup
GRCh37.p13 chr 5	NC_000005.9:g.150837873GT[3]
GRCh37.p13 chr 5	NC_000005.9:g.150837873GT[4]

Gene: SLC36A1, solute carrier family 36 member 1 (plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
SLC36A1 transcript variant 2	NM_001308150.2:c.-5-476_-… NM_001308150.2:c.-5-476_-5-475dup	N/A	Intron Variant
SLC36A1 transcript variant 3	NM_001308151.2:c.-5-476_-… NM_001308151.2:c.-5-476_-5-475dup	N/A	Intron Variant
SLC36A1 transcript variant 4	NM_001349740.2:c.-148-476… NM_001349740.2:c.-148-476_-148-475dup	N/A	Intron Variant
SLC36A1 transcript variant 1	NM_078483.4:c.-5-476_-5-4… NM_078483.4:c.-5-476_-5-475dup	N/A	Intron Variant
SLC36A1 transcript variant X2	XM_011537580.3:c.14-476_1… XM_011537580.3:c.14-476_14-475dup	N/A	Intron Variant
SLC36A1 transcript variant X3	XM_011537581.2:c.-5-476_-… XM_011537581.2:c.-5-476_-5-475dup	N/A	Intron Variant
SLC36A1 transcript variant X10	XM_011537584.3:c.-5-476_-… XM_011537584.3:c.-5-476_-5-475dup	N/A	Intron Variant
SLC36A1 transcript variant X5	XM_011537585.1:c.-5-476_-… XM_011537585.1:c.-5-476_-5-475dup	N/A	Intron Variant
SLC36A1 transcript variant X6	XM_011537586.3:c.-5-476_-… XM_011537586.3:c.-5-476_-5-475dup	N/A	Intron Variant
SLC36A1 transcript variant X21	XM_011537587.4:c.-5-476_-… XM_011537587.4:c.-5-476_-5-475dup	N/A	Intron Variant
SLC36A1 transcript variant X7	XM_011537589.4:c.-5-476_-… XM_011537589.4:c.-5-476_-5-475dup	N/A	Intron Variant
SLC36A1 transcript variant X9	XM_011537590.2:c.-5-476_-… XM_011537590.2:c.-5-476_-5-475dup	N/A	Intron Variant
SLC36A1 transcript variant X11	XM_011537591.2:c.-5-476_-… XM_011537591.2:c.-5-476_-5-475dup	N/A	Intron Variant
SLC36A1 transcript variant X12	XM_011537592.3:c.-5-476_-… XM_011537592.3:c.-5-476_-5-475dup	N/A	Intron Variant
SLC36A1 transcript variant X13	XM_017009216.2:c.-5-476_-… XM_017009216.2:c.-5-476_-5-475dup	N/A	Intron Variant
SLC36A1 transcript variant X18	XM_017009217.2:c.-5-476_-… XM_017009217.2:c.-5-476_-5-475dup	N/A	Intron Variant
SLC36A1 transcript variant X4	XM_047416921.1:c.-5-476_-… XM_047416921.1:c.-5-476_-5-475dup	N/A	Intron Variant
SLC36A1 transcript variant X8	XM_047416923.1:c.-5-476_-… XM_047416923.1:c.-5-476_-5-475dup	N/A	Intron Variant
SLC36A1 transcript variant X14	XM_047416924.1:c.-5-476_-… XM_047416924.1:c.-5-476_-5-475dup	N/A	Intron Variant
SLC36A1 transcript variant X19	XM_047416928.1:c.14-476_1… XM_047416928.1:c.14-476_14-475dup	N/A	Intron Variant
SLC36A1 transcript variant X1	XM_047416920.1:c.-388_-38… XM_047416920.1:c.-388_-387=	N/A	5 Prime UTR Variant
SLC36A1 transcript variant X15	XM_047416925.1:c.-388_-38… XM_047416925.1:c.-388_-387=	N/A	5 Prime UTR Variant
SLC36A1 transcript variant X16	XM_011537595.3:c.-388_-38… XM_011537595.3:c.-388_-387=	N/A	5 Prime UTR Variant
SLC36A1 transcript variant X17	XM_047416927.1:c.-388_-38… XM_047416927.1:c.-388_-387=	N/A	5 Prime UTR Variant
SLC36A1 transcript variant X22	XM_011537596.3:c.-388_-38… XM_011537596.3:c.-388_-387=	N/A	5 Prime UTR Variant
SLC36A1 transcript variant X23	XM_047416929.1:c.-388_-38… XM_047416929.1:c.-388_-387=	N/A	5 Prime UTR Variant
SLC36A1 transcript variant X20	XM_006714759.5:c.	N/A	Genic Upstream Transcript Variant

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

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".

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#.

11 SubSNP, 8 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	KOGIC	ss3957909255	Apr 26, 2020 (154)
2	KOGIC	ss3957909256	Apr 26, 2020 (154)
3	GNOMAD	ss4131778933	Apr 26, 2021 (155)
4	GNOMAD	ss4131778934	Apr 26, 2021 (155)
5	GNOMAD	ss4131778935	Apr 26, 2021 (155)
6	TOMMO_GENOMICS	ss5174766752	Apr 26, 2021 (155)
7	TOMMO_GENOMICS	ss5174766754	Apr 26, 2021 (155)
8	1000G_HIGH_COVERAGE	ss5266325281	Oct 13, 2022 (156)
9	1000G_HIGH_COVERAGE	ss5266325282	Oct 13, 2022 (156)
10	HUGCELL_USP	ss5464241834	Oct 13, 2022 (156)
11	HUGCELL_USP	ss5464241835	Oct 13, 2022 (156)
12	gnomAD - Genomes Submission ignored due to conflicting rows: Row 208412133 (NC_000005.10:151458311::GT 2/40904) Row 208412134 (NC_000005.10:151458311::GTGT 346/40860) Row 208412135 (NC_000005.10:151458311::GTGTGT 112/40902)	-	Apr 26, 2021 (155)
13	gnomAD - Genomes Submission ignored due to conflicting rows: Row 208412133 (NC_000005.10:151458311::GT 2/40904) Row 208412134 (NC_000005.10:151458311::GTGT 346/40860) Row 208412135 (NC_000005.10:151458311::GTGTGT 112/40902)	-	Apr 26, 2021 (155)
14	gnomAD - Genomes Submission ignored due to conflicting rows: Row 208412133 (NC_000005.10:151458311::GT 2/40904) Row 208412134 (NC_000005.10:151458311::GTGT 346/40860) Row 208412135 (NC_000005.10:151458311::GTGTGT 112/40902)	-	Apr 26, 2021 (155)
15	Korean Genome Project Submission ignored due to conflicting rows: Row 14287256 (NC_000005.10:151458313::GTGT 59/1820) Row 14287257 (NC_000005.10:151458313::GTGTGT 1/1820)	-	Apr 26, 2020 (154)
16	Korean Genome Project Submission ignored due to conflicting rows: Row 14287256 (NC_000005.10:151458313::GTGT 59/1820) Row 14287257 (NC_000005.10:151458313::GTGTGT 1/1820)	-	Apr 26, 2020 (154)
17	8.3KJPN Submission ignored due to conflicting rows: Row 32736059 (NC_000005.9:150837872::GTGT 222/16670) Row 32736061 (NC_000005.9:150837872::GTGTGT 8/16670)	-	Apr 26, 2021 (155)
18	8.3KJPN Submission ignored due to conflicting rows: Row 32736059 (NC_000005.9:150837872::GTGT 222/16670) Row 32736061 (NC_000005.9:150837872::GTGTGT 8/16670)	-	Apr 26, 2021 (155)
19	ALFA	NC_000005.10 - 151458312	Apr 26, 2021 (155)

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
ss4131778933	NC_000005.10:151458311::GT	NC_000005.10:151458311:GT:GTGT	(self)
5066480155	NC_000005.10:151458311:GT:GTGT	NC_000005.10:151458311:GT:GTGT	(self)
ss5174766752	NC_000005.9:150837872::GTGT	NC_000005.10:151458311:GT:GTGTGT	(self)
ss4131778934, ss5266325282, ss5464241834	NC_000005.10:151458311::GTGT	NC_000005.10:151458311:GT:GTGTGT	(self)
ss3957909255	NC_000005.10:151458313::GTGT	NC_000005.10:151458311:GT:GTGTGT	(self)
ss5174766754	NC_000005.9:150837872::GTGTGT	NC_000005.10:151458311:GT:GTGTGTGT	(self)
ss4131778935, ss5266325281, ss5464241835	NC_000005.10:151458311::GTGTGT	NC_000005.10:151458311:GT:GTGTGTGT	(self)
ss3957909256	NC_000005.10:151458313::GTGTGT	NC_000005.10:151458311:GT:GTGTGTGT	(self)

Publications tab displays PubMed articles citing the variation as a listing of PMID, Title, Author, Year, Journal, ordered by Year, descending.

No publications for rs1491554377

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.

Choose placement

Placement	GT=	dupGT	insGTGT	ins(GT)₃
GRCh38.p14 chr 5	NC_000005.10:g.151458312_151458313=	NC_000005.10:g.151458312_151458313dup	NC_000005.10:g.151458312GT[3]	NC_000005.10:g.151458312GT[4]
GRCh37.p13 chr 5	NC_000005.9:g.150837873_150837874=	NC_000005.9:g.150837873_150837874dup	NC_000005.9:g.150837873GT[3]	NC_000005.9:g.150837873GT[4]
SLC36A1 transcript variant X16	XM_011537595.3:c.-388_-387=	XM_011537595.3:c.-388_-387dup	XM_011537595.3:c.-388GT[3]	XM_011537595.3:c.-388GT[4]
SLC36A1 transcript variant X22	XM_011537596.3:c.-388_-387=	XM_011537596.3:c.-388_-387dup	XM_011537596.3:c.-388GT[3]	XM_011537596.3:c.-388GT[4]
SLC36A1 transcript variant X17	XM_047416927.1:c.-388_-387=	XM_047416927.1:c.-388_-387dup	XM_047416927.1:c.-388GT[3]	XM_047416927.1:c.-388GT[4]
SLC36A1 transcript variant X1	XM_047416920.1:c.-388_-387=	XM_047416920.1:c.-388_-387dup	XM_047416920.1:c.-388GT[3]	XM_047416920.1:c.-388GT[4]
SLC36A1 transcript variant X15	XM_047416925.1:c.-388_-387=	XM_047416925.1:c.-388_-387dup	XM_047416925.1:c.-388GT[3]	XM_047416925.1:c.-388GT[4]
SLC36A1 transcript variant X23	XM_047416929.1:c.-388_-387=	XM_047416929.1:c.-388_-387dup	XM_047416929.1:c.-388GT[3]	XM_047416929.1:c.-388GT[4]
SLC36A1 transcript variant 2	NM_001308150.2:c.-5-476=	NM_001308150.2:c.-5-476_-5-475dup	NM_001308150.2:c.-5-475_-5-474insGTGT	NM_001308150.2:c.-5-475_-5-474insGTGTGT
SLC36A1 transcript variant 3	NM_001308151.2:c.-5-476=	NM_001308151.2:c.-5-476_-5-475dup	NM_001308151.2:c.-5-475_-5-474insGTGT	NM_001308151.2:c.-5-475_-5-474insGTGTGT
SLC36A1 transcript variant 4	NM_001349740.2:c.-148-476=	NM_001349740.2:c.-148-476_-148-475dup	NM_001349740.2:c.-148-475_-148-474insGTGT	NM_001349740.2:c.-148-475_-148-474insGTGTGT
SLC36A1 transcript	NM_078483.2:c.-5-476=	NM_078483.2:c.-5-476_-5-475dup	NM_078483.2:c.-5-475_-5-474insGTGT	NM_078483.2:c.-5-475_-5-474insGTGTGT
SLC36A1 transcript variant 1	NM_078483.4:c.-5-476=	NM_078483.4:c.-5-476_-5-475dup	NM_078483.4:c.-5-475_-5-474insGTGT	NM_078483.4:c.-5-475_-5-474insGTGTGT
SLC36A1 transcript variant X7	XM_005268386.1:c.-5-476=	XM_005268386.1:c.-5-476_-5-475dup	XM_005268386.1:c.-5-475_-5-474insGTGT	XM_005268386.1:c.-5-475_-5-474insGTGTGT
SLC36A1 transcript variant X2	XM_005268387.1:c.-5-476=	XM_005268387.1:c.-5-476_-5-475dup	XM_005268387.1:c.-5-475_-5-474insGTGT	XM_005268387.1:c.-5-475_-5-474insGTGTGT
SLC36A1 transcript variant X3	XM_005268388.1:c.-5-476=	XM_005268388.1:c.-5-476_-5-475dup	XM_005268388.1:c.-5-475_-5-474insGTGT	XM_005268388.1:c.-5-475_-5-474insGTGTGT
SLC36A1 transcript variant X2	XM_011537580.3:c.14-476=	XM_011537580.3:c.14-476_14-475dup	XM_011537580.3:c.14-475_14-474insGTGT	XM_011537580.3:c.14-475_14-474insGTGTGT
SLC36A1 transcript variant X3	XM_011537581.2:c.-5-476=	XM_011537581.2:c.-5-476_-5-475dup	XM_011537581.2:c.-5-475_-5-474insGTGT	XM_011537581.2:c.-5-475_-5-474insGTGTGT
SLC36A1 transcript variant X10	XM_011537584.3:c.-5-476=	XM_011537584.3:c.-5-476_-5-475dup	XM_011537584.3:c.-5-475_-5-474insGTGT	XM_011537584.3:c.-5-475_-5-474insGTGTGT
SLC36A1 transcript variant X5	XM_011537585.1:c.-5-476=	XM_011537585.1:c.-5-476_-5-475dup	XM_011537585.1:c.-5-475_-5-474insGTGT	XM_011537585.1:c.-5-475_-5-474insGTGTGT
SLC36A1 transcript variant X6	XM_011537586.3:c.-5-476=	XM_011537586.3:c.-5-476_-5-475dup	XM_011537586.3:c.-5-475_-5-474insGTGT	XM_011537586.3:c.-5-475_-5-474insGTGTGT
SLC36A1 transcript variant X21	XM_011537587.4:c.-5-476=	XM_011537587.4:c.-5-476_-5-475dup	XM_011537587.4:c.-5-475_-5-474insGTGT	XM_011537587.4:c.-5-475_-5-474insGTGTGT
SLC36A1 transcript variant X7	XM_011537589.4:c.-5-476=	XM_011537589.4:c.-5-476_-5-475dup	XM_011537589.4:c.-5-475_-5-474insGTGT	XM_011537589.4:c.-5-475_-5-474insGTGTGT
SLC36A1 transcript variant X9	XM_011537590.2:c.-5-476=	XM_011537590.2:c.-5-476_-5-475dup	XM_011537590.2:c.-5-475_-5-474insGTGT	XM_011537590.2:c.-5-475_-5-474insGTGTGT
SLC36A1 transcript variant X11	XM_011537591.2:c.-5-476=	XM_011537591.2:c.-5-476_-5-475dup	XM_011537591.2:c.-5-475_-5-474insGTGT	XM_011537591.2:c.-5-475_-5-474insGTGTGT
SLC36A1 transcript variant X12	XM_011537592.3:c.-5-476=	XM_011537592.3:c.-5-476_-5-475dup	XM_011537592.3:c.-5-475_-5-474insGTGT	XM_011537592.3:c.-5-475_-5-474insGTGTGT
SLC36A1 transcript variant X13	XM_017009216.2:c.-5-476=	XM_017009216.2:c.-5-476_-5-475dup	XM_017009216.2:c.-5-475_-5-474insGTGT	XM_017009216.2:c.-5-475_-5-474insGTGTGT
SLC36A1 transcript variant X18	XM_017009217.2:c.-5-476=	XM_017009217.2:c.-5-476_-5-475dup	XM_017009217.2:c.-5-475_-5-474insGTGT	XM_017009217.2:c.-5-475_-5-474insGTGTGT
SLC36A1 transcript variant X4	XM_047416921.1:c.-5-476=	XM_047416921.1:c.-5-476_-5-475dup	XM_047416921.1:c.-5-475_-5-474insGTGT	XM_047416921.1:c.-5-475_-5-474insGTGTGT
SLC36A1 transcript variant X8	XM_047416923.1:c.-5-476=	XM_047416923.1:c.-5-476_-5-475dup	XM_047416923.1:c.-5-475_-5-474insGTGT	XM_047416923.1:c.-5-475_-5-474insGTGTGT
SLC36A1 transcript variant X14	XM_047416924.1:c.-5-476=	XM_047416924.1:c.-5-476_-5-475dup	XM_047416924.1:c.-5-475_-5-474insGTGT	XM_047416924.1:c.-5-475_-5-474insGTGTGT
SLC36A1 transcript variant X19	XM_047416928.1:c.14-476=	XM_047416928.1:c.14-476_14-475dup	XM_047416928.1:c.14-475_14-474insGTGT	XM_047416928.1:c.14-475_14-474insGTGTGT

dbSNP Short Genetic Variations

Welcome to the Reference SNP (rs) Report

Reference SNP (rs) Report

rs1491554377