Name: rs1491400003
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.

rs1491400003

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr11:62870850-62870851 (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: insTAT / ins(TAT)₂ / ins(TAT)₃ / i…
insTAT / ins(TAT)₂ / ins(TAT)₃ / ins(TAT)₄
Variation Type: Indel Insertion and Deletion
Frequency: insTAT=0.00000 (0/11810, ALFA)
ins(TAT)₂=0.00000 (0/11810, ALFA)
ins(TAT)₃=0.00000 (0/11810, ALFA) (+ 1 more)
ins(TAT)₄=0.00000 (0/11810, ALFA)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: SLC3A2 : 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	11810	AT=1.00000	ATTAT=0.00000, ATTATTAT=0.00000, ATTATTATTAT=0.00000, ATTATTATTATTAT=0.00000	1.0	N/A
European	Sub	7582	AT=1.0000	ATTAT=0.0000, ATTATTAT=0.0000, ATTATTATTAT=0.0000, ATTATTATTATTAT=0.0000	1.0	N/A
African	Sub	2802	AT=1.0000	ATTAT=0.0000, ATTATTAT=0.0000, ATTATTATTAT=0.0000, ATTATTATTATTAT=0.0000	1.0	N/A
African Others	Sub	108	AT=1.000	ATTAT=0.000, ATTATTAT=0.000, ATTATTATTAT=0.000, ATTATTATTATTAT=0.000	1.0	N/A
African American	Sub	2694	AT=1.0000	ATTAT=0.0000, ATTATTAT=0.0000, ATTATTATTAT=0.0000, ATTATTATTATTAT=0.0000	1.0	N/A
Asian	Sub	108	AT=1.000	ATTAT=0.000, ATTATTAT=0.000, ATTATTATTAT=0.000, ATTATTATTATTAT=0.000	1.0	N/A
East Asian	Sub	84	AT=1.00	ATTAT=0.00, ATTATTAT=0.00, ATTATTATTAT=0.00, ATTATTATTATTAT=0.00	1.0	N/A
Other Asian	Sub	24	AT=1.00	ATTAT=0.00, ATTATTAT=0.00, ATTATTATTAT=0.00, ATTATTATTATTAT=0.00	1.0	N/A
Latin American 1	Sub	146	AT=1.000	ATTAT=0.000, ATTATTAT=0.000, ATTATTATTAT=0.000, ATTATTATTATTAT=0.000	1.0	N/A
Latin American 2	Sub	610	AT=1.000	ATTAT=0.000, ATTATTAT=0.000, ATTATTATTAT=0.000, ATTATTATTATTAT=0.000	1.0	N/A
South Asian	Sub	94	AT=1.00	ATTAT=0.00, ATTATTAT=0.00, ATTATTATTAT=0.00, ATTATTATTATTAT=0.00	1.0	N/A
Other	Sub	468	AT=1.000	ATTAT=0.000, ATTATTAT=0.000, ATTATTATTAT=0.000, ATTATTATTATTAT=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	11810	AT=1.00000	insTAT=0.00000, ins(TAT)₂=0.00000, ins(TAT)₃=0.00000, ins(TAT)₄=0.00000
Allele Frequency Aggregator	European	Sub	7582	AT=1.0000	insTAT=0.0000, ins(TAT)₂=0.0000, ins(TAT)₃=0.0000, ins(TAT)₄=0.0000
Allele Frequency Aggregator	African	Sub	2802	AT=1.0000	insTAT=0.0000, ins(TAT)₂=0.0000, ins(TAT)₃=0.0000, ins(TAT)₄=0.0000
Allele Frequency Aggregator	Latin American 2	Sub	610	AT=1.000	insTAT=0.000, ins(TAT)₂=0.000, ins(TAT)₃=0.000, ins(TAT)₄=0.000
Allele Frequency Aggregator	Other	Sub	468	AT=1.000	insTAT=0.000, ins(TAT)₂=0.000, ins(TAT)₃=0.000, ins(TAT)₄=0.000
Allele Frequency Aggregator	Latin American 1	Sub	146	AT=1.000	insTAT=0.000, ins(TAT)₂=0.000, ins(TAT)₃=0.000, ins(TAT)₄=0.000
Allele Frequency Aggregator	Asian	Sub	108	AT=1.000	insTAT=0.000, ins(TAT)₂=0.000, ins(TAT)₃=0.000, ins(TAT)₄=0.000
Allele Frequency Aggregator	South Asian	Sub	94	AT=1.00	insTAT=0.00, ins(TAT)₂=0.00, ins(TAT)₃=0.00, ins(TAT)₄=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 11	NC_000011.10:g.62870851_62870852insTAT
GRCh38.p14 chr 11	NC_000011.10:g.62870851_62870852insTATTAT
GRCh38.p14 chr 11	NC_000011.10:g.62870852TAT[3]
GRCh38.p14 chr 11	NC_000011.10:g.62870852TAT[4]
GRCh37.p13 chr 11	NC_000011.9:g.62638323_62638324insTAT
GRCh37.p13 chr 11	NC_000011.9:g.62638323_62638324insTATTAT
GRCh37.p13 chr 11	NC_000011.9:g.62638324TAT[3]
GRCh37.p13 chr 11	NC_000011.9:g.62638324TAT[4]

Gene: SLC3A2, solute carrier family 3 member 2 (plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
SLC3A2 transcript variant 2	NM_001012662.3:c.113-726_… NM_001012662.3:c.113-726_113-725insTAT	N/A	Intron Variant
SLC3A2 transcript variant 5	NM_001012664.3:c.113-1016… NM_001012664.3:c.113-10168_113-10167insTAT	N/A	Intron Variant
SLC3A2 transcript variant 3	NM_002394.6:c.205+14_205+… NM_002394.6:c.205+14_205+15insTAT	N/A	Intron Variant
SLC3A2 transcript variant 6	NM_001013251.3:c.	N/A	Genic Upstream Transcript Variant
SLC3A2 transcript variant 7	NR_037193.2:n.	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".

Placement	AT=	insTAT	ins(TAT)₂	ins(TAT)₃	ins(TAT)₄
GRCh38.p14 chr 11	NC_000011.10:g.62870850_62870851=	NC_000011.10:g.62870851_62870852insTAT	NC_000011.10:g.62870851_62870852insTATTAT	NC_000011.10:g.62870852TAT[3]	NC_000011.10:g.62870852TAT[4]
GRCh37.p13 chr 11	NC_000011.9:g.62638322_62638323=	NC_000011.9:g.62638323_62638324insTAT	NC_000011.9:g.62638323_62638324insTATTAT	NC_000011.9:g.62638324TAT[3]	NC_000011.9:g.62638324TAT[4]
SLC3A2 transcript variant 2	NM_001012662.2:c.113-727=	NM_001012662.2:c.113-726_113-725insTAT	NM_001012662.2:c.113-726_113-725insTATTAT	NM_001012662.2:c.113-726_113-725insTATTATTAT	NM_001012662.2:c.113-726_113-725insTATTATTATTAT
SLC3A2 transcript variant 2	NM_001012662.3:c.113-727=	NM_001012662.3:c.113-726_113-725insTAT	NM_001012662.3:c.113-726_113-725insTATTAT	NM_001012662.3:c.113-726_113-725insTATTATTAT	NM_001012662.3:c.113-726_113-725insTATTATTATTAT
SLC3A2 transcript variant 5	NM_001012664.2:c.113-10169=	NM_001012664.2:c.113-10168_113-10167insTAT	NM_001012664.2:c.113-10168_113-10167insTATTAT	NM_001012664.2:c.113-10168_113-10167insTATTATTAT	NM_001012664.2:c.113-10168_113-10167insTATTATTATTAT
SLC3A2 transcript variant 5	NM_001012664.3:c.113-10169=	NM_001012664.3:c.113-10168_113-10167insTAT	NM_001012664.3:c.113-10168_113-10167insTATTAT	NM_001012664.3:c.113-10168_113-10167insTATTATTAT	NM_001012664.3:c.113-10168_113-10167insTATTATTATTAT
SLC3A2 transcript variant 3	NM_002394.5:c.205+13=	NM_002394.5:c.205+14_205+15insTAT	NM_002394.5:c.205+14_205+15insTATTAT	NM_002394.5:c.205+14_205+15insTATTATTAT	NM_002394.5:c.205+14_205+15insTATTATTATTAT
SLC3A2 transcript variant 3	NM_002394.6:c.205+13=	NM_002394.6:c.205+14_205+15insTAT	NM_002394.6:c.205+14_205+15insTATTAT	NM_002394.6:c.205+14_205+15insTATTATTAT	NM_002394.6:c.205+14_205+15insTATTATTATTAT

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	EVA_DECODE	ss3691921636	Jul 13, 2019 (153)
2	ALFA	NC_000011.10 - 62870850	Apr 27, 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
1275624520	NC_000011.10:62870849:AT:ATTAT	NC_000011.10:62870849:AT:ATTAT	(self)
ss3691921636	NC_000011.10:62870851::TAT	NC_000011.10:62870849:AT:ATTAT	(self)
1275624520	NC_000011.10:62870849:AT:ATTATTAT	NC_000011.10:62870849:AT:ATTATTAT	(self)
1275624520	NC_000011.10:62870849:AT:ATTATTATT… NC_000011.10:62870849:AT:ATTATTATTAT	NC_000011.10:62870849:AT:ATTATTATT… NC_000011.10:62870849:AT:ATTATTATTAT	(self)
1275624520	NC_000011.10:62870849:AT:ATTATTATT… NC_000011.10:62870849:AT:ATTATTATTATTAT	NC_000011.10:62870849:AT:ATTATTATT… NC_000011.10:62870849:AT:ATTATTATTATTAT	(self)

Removed from this RefSNP Cluster:

Submission IDs	Observation SPDI	Canonical SPDI	Destination RSIDs
ss3147190965	NC_000011.10:62870849::ATT	NC_000011.10:62870849:AT:ATTAT
ss3147190966	NC_000011.10:62870849::ATTATT	NC_000011.10:62870849:AT:ATTATTAT

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

No publications for rs1491400003

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

dbSNP Short Genetic Variations

Welcome to the Reference SNP (rs) Report

Reference SNP (rs) Report

rs1491400003