Name: rs113166440
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.

rs113166440

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr5:151497940-151497952 (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: delTT / delT / dupT / dupTT / dupT…
delTT / delT / dupT / dupTT / dupTTT / dup(T)₄
Variation Type: Indel Insertion and Deletion
Frequency: dupTTT=0.00106 (17/16112, 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	HTRZ	HWEP
Total	Global	16112	TTTTTTTTTTTTT=0.99801	TTTTTTTTTTTT=0.00062, TTTTTTTTTTTTTT=0.00006, TTTTTTTTTTTTTTT=0.00000, TTTTTTTTTTTTTTTT=0.00106, TTTTTTTTTTTTTTTTT=0.00025	0.997886	0.002114	0
European	Sub	12044	TTTTTTTTTTTTT=0.99734	TTTTTTTTTTTT=0.00083, TTTTTTTTTTTTTT=0.00008, TTTTTTTTTTTTTTT=0.00000, TTTTTTTTTTTTTTTT=0.00141, TTTTTTTTTTTTTTTTT=0.00033	0.99717	0.00283	0
African	Sub	2662	TTTTTTTTTTTTT=1.0000	TTTTTTTTTTTT=0.0000, TTTTTTTTTTTTTT=0.0000, TTTTTTTTTTTTTTT=0.0000, TTTTTTTTTTTTTTTT=0.0000, TTTTTTTTTTTTTTTTT=0.0000	1.0	0.0	N/A
African Others	Sub	98	TTTTTTTTTTTTT=1.00	TTTTTTTTTTTT=0.00, TTTTTTTTTTTTTT=0.00, TTTTTTTTTTTTTTT=0.00, TTTTTTTTTTTTTTTT=0.00, TTTTTTTTTTTTTTTTT=0.00	1.0	0.0	N/A
African American	Sub	2564	TTTTTTTTTTTTT=1.0000	TTTTTTTTTTTT=0.0000, TTTTTTTTTTTTTT=0.0000, TTTTTTTTTTTTTTT=0.0000, TTTTTTTTTTTTTTTT=0.0000, TTTTTTTTTTTTTTTTT=0.0000	1.0	0.0	N/A
Asian	Sub	106	TTTTTTTTTTTTT=1.000	TTTTTTTTTTTT=0.000, TTTTTTTTTTTTTT=0.000, TTTTTTTTTTTTTTT=0.000, TTTTTTTTTTTTTTTT=0.000, TTTTTTTTTTTTTTTTT=0.000	1.0	0.0	N/A
East Asian	Sub	82	TTTTTTTTTTTTT=1.00	TTTTTTTTTTTT=0.00, TTTTTTTTTTTTTT=0.00, TTTTTTTTTTTTTTT=0.00, TTTTTTTTTTTTTTTT=0.00, TTTTTTTTTTTTTTTTT=0.00	1.0	0.0	N/A
Other Asian	Sub	24	TTTTTTTTTTTTT=1.00	TTTTTTTTTTTT=0.00, TTTTTTTTTTTTTT=0.00, TTTTTTTTTTTTTTT=0.00, TTTTTTTTTTTTTTTT=0.00, TTTTTTTTTTTTTTTTT=0.00	1.0	0.0	N/A
Latin American 1	Sub	138	TTTTTTTTTTTTT=1.000	TTTTTTTTTTTT=0.000, TTTTTTTTTTTTTT=0.000, TTTTTTTTTTTTTTT=0.000, TTTTTTTTTTTTTTTT=0.000, TTTTTTTTTTTTTTTTT=0.000	1.0	0.0	N/A
Latin American 2	Sub	606	TTTTTTTTTTTTT=1.000	TTTTTTTTTTTT=0.000, TTTTTTTTTTTTTT=0.000, TTTTTTTTTTTTTTT=0.000, TTTTTTTTTTTTTTTT=0.000, TTTTTTTTTTTTTTTTT=0.000	1.0	0.0	N/A
South Asian	Sub	94	TTTTTTTTTTTTT=1.00	TTTTTTTTTTTT=0.00, TTTTTTTTTTTTTT=0.00, TTTTTTTTTTTTTTT=0.00, TTTTTTTTTTTTTTTT=0.00, TTTTTTTTTTTTTTTTT=0.00	1.0	0.0	N/A
Other	Sub	462	TTTTTTTTTTTTT=1.000	TTTTTTTTTTTT=0.000, TTTTTTTTTTTTTT=0.000, TTTTTTTTTTTTTTT=0.000, TTTTTTTTTTTTTTTT=0.000, TTTTTTTTTTTTTTTTT=0.000	1.0	0.0	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	16112	(T)₁₃=0.99801	delT=0.00062, dupT=0.00006, dupTT=0.00000, dupTTT=0.00106, dup(T)₄=0.00025
Allele Frequency Aggregator	European	Sub	12044	(T)₁₃=0.99734	delT=0.00083, dupT=0.00008, dupTT=0.00000, dupTTT=0.00141, dup(T)₄=0.00033
Allele Frequency Aggregator	African	Sub	2662	(T)₁₃=1.0000	delT=0.0000, dupT=0.0000, dupTT=0.0000, dupTTT=0.0000, dup(T)₄=0.0000
Allele Frequency Aggregator	Latin American 2	Sub	606	(T)₁₃=1.000	delT=0.000, dupT=0.000, dupTT=0.000, dupTTT=0.000, dup(T)₄=0.000
Allele Frequency Aggregator	Other	Sub	462	(T)₁₃=1.000	delT=0.000, dupT=0.000, dupTT=0.000, dupTTT=0.000, dup(T)₄=0.000
Allele Frequency Aggregator	Latin American 1	Sub	138	(T)₁₃=1.000	delT=0.000, dupT=0.000, dupTT=0.000, dupTTT=0.000, dup(T)₄=0.000
Allele Frequency Aggregator	Asian	Sub	106	(T)₁₃=1.000	delT=0.000, dupT=0.000, dupTT=0.000, dupTTT=0.000, dup(T)₄=0.000
Allele Frequency Aggregator	South Asian	Sub	94	(T)₁₃=1.00	delT=0.00, dupT=0.00, dupTT=0.00, dupTTT=0.00, dup(T)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 5	NC_000005.10:g.151497951_151497952del
GRCh38.p14 chr 5	NC_000005.10:g.151497952del
GRCh38.p14 chr 5	NC_000005.10:g.151497952dup
GRCh38.p14 chr 5	NC_000005.10:g.151497951_151497952dup
GRCh38.p14 chr 5	NC_000005.10:g.151497950_151497952dup
GRCh38.p14 chr 5	NC_000005.10:g.151497949_151497952dup
GRCh37.p13 chr 5	NC_000005.9:g.150877512_150877513del
GRCh37.p13 chr 5	NC_000005.9:g.150877513del
GRCh37.p13 chr 5	NC_000005.9:g.150877513dup
GRCh37.p13 chr 5	NC_000005.9:g.150877512_150877513dup
GRCh37.p13 chr 5	NC_000005.9:g.150877511_150877513dup
GRCh37.p13 chr 5	NC_000005.9:g.150877510_150877513dup

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.	N/A	Genic Downstream Transcript Variant
SLC36A1 transcript variant 3	NM_001308151.2:c.	N/A	Genic Downstream Transcript Variant
SLC36A1 transcript variant 4	NM_001349740.2:c.	N/A	Genic Downstream Transcript Variant
SLC36A1 transcript variant 1	NM_078483.4:c.	N/A	Genic Downstream Transcript Variant
SLC36A1 transcript variant X16	XM_011537595.3:c.1252+184… XM_011537595.3:c.1252+18462_1252+18463del	N/A	Intron Variant
SLC36A1 transcript variant X18	XM_017009217.2:c.1159+184… XM_017009217.2:c.1159+18462_1159+18463del	N/A	Intron Variant
SLC36A1 transcript variant X15	XM_047416925.1:c.1252+184… XM_047416925.1:c.1252+18462_1252+18463del	N/A	Intron Variant
SLC36A1 transcript variant X20	XM_006714759.5:c.	N/A	Genic Downstream Transcript Variant
SLC36A1 transcript variant X2	XM_011537580.3:c.	N/A	Genic Downstream Transcript Variant
SLC36A1 transcript variant X3	XM_011537581.2:c.	N/A	Genic Downstream Transcript Variant
SLC36A1 transcript variant X10	XM_011537584.3:c.	N/A	Genic Downstream Transcript Variant
SLC36A1 transcript variant X5	XM_011537585.1:c.	N/A	Genic Downstream Transcript Variant
SLC36A1 transcript variant X6	XM_011537586.3:c.	N/A	Genic Downstream Transcript Variant
SLC36A1 transcript variant X21	XM_011537587.4:c.	N/A	Genic Downstream Transcript Variant
SLC36A1 transcript variant X7	XM_011537589.4:c.	N/A	Genic Downstream Transcript Variant
SLC36A1 transcript variant X9	XM_011537590.2:c.	N/A	Genic Downstream Transcript Variant
SLC36A1 transcript variant X11	XM_011537591.2:c.	N/A	Genic Downstream Transcript Variant
SLC36A1 transcript variant X12	XM_011537592.3:c.	N/A	Genic Downstream Transcript Variant
SLC36A1 transcript variant X22	XM_011537596.3:c.	N/A	Genic Downstream Transcript Variant
SLC36A1 transcript variant X13	XM_017009216.2:c.	N/A	Genic Downstream Transcript Variant
SLC36A1 transcript variant X1	XM_047416920.1:c.	N/A	Genic Downstream Transcript Variant
SLC36A1 transcript variant X4	XM_047416921.1:c.	N/A	Genic Downstream Transcript Variant
SLC36A1 transcript variant X8	XM_047416923.1:c.	N/A	Genic Downstream Transcript Variant
SLC36A1 transcript variant X14	XM_047416924.1:c.	N/A	Genic Downstream Transcript Variant
SLC36A1 transcript variant X17	XM_047416927.1:c.	N/A	Genic Downstream Transcript Variant
SLC36A1 transcript variant X19	XM_047416928.1:c.	N/A	Genic Downstream Transcript Variant
SLC36A1 transcript variant X23	XM_047416929.1:c.	N/A	Genic Downstream 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	(T)₁₃=	delTT	delT	dupT	dupTT	dupTTT	dup(T)₄
GRCh38.p14 chr 5	NC_000005.10:g.151497940_151497952=	NC_000005.10:g.151497951_151497952del	NC_000005.10:g.151497952del	NC_000005.10:g.151497952dup	NC_000005.10:g.151497951_151497952dup	NC_000005.10:g.151497950_151497952dup	NC_000005.10:g.151497949_151497952dup
GRCh37.p13 chr 5	NC_000005.9:g.150877501_150877513=	NC_000005.9:g.150877512_150877513del	NC_000005.9:g.150877513del	NC_000005.9:g.150877513dup	NC_000005.9:g.150877512_150877513dup	NC_000005.9:g.150877511_150877513dup	NC_000005.9:g.150877510_150877513dup
SLC36A1 transcript variant X16	XM_011537595.3:c.1252+18451=	XM_011537595.3:c.1252+18462_1252+18463del	XM_011537595.3:c.1252+18463del	XM_011537595.3:c.1252+18463dup	XM_011537595.3:c.1252+18462_1252+18463dup	XM_011537595.3:c.1252+18461_1252+18463dup	XM_011537595.3:c.1252+18460_1252+18463dup
SLC36A1 transcript variant X18	XM_017009217.2:c.1159+18451=	XM_017009217.2:c.1159+18462_1159+18463del	XM_017009217.2:c.1159+18463del	XM_017009217.2:c.1159+18463dup	XM_017009217.2:c.1159+18462_1159+18463dup	XM_017009217.2:c.1159+18461_1159+18463dup	XM_017009217.2:c.1159+18460_1159+18463dup
SLC36A1 transcript variant X15	XM_047416925.1:c.1252+18451=	XM_047416925.1:c.1252+18462_1252+18463del	XM_047416925.1:c.1252+18463del	XM_047416925.1:c.1252+18463dup	XM_047416925.1:c.1252+18462_1252+18463dup	XM_047416925.1:c.1252+18461_1252+18463dup	XM_047416925.1:c.1252+18460_1252+18463dup

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#.

17 SubSNP, 9 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	BUSHMAN	ss193829977	Jul 04, 2010 (132)
2	SWEGEN	ss2998012978	Nov 08, 2017 (151)
3	GNOMAD	ss4131783867	Apr 26, 2021 (155)
4	GNOMAD	ss4131783868	Apr 26, 2021 (155)
5	GNOMAD	ss4131783869	Apr 26, 2021 (155)
6	GNOMAD	ss4131783870	Apr 26, 2021 (155)
7	TOMMO_GENOMICS	ss5174768024	Apr 26, 2021 (155)
8	TOMMO_GENOMICS	ss5174768025	Apr 26, 2021 (155)
9	1000G_HIGH_COVERAGE	ss5266326267	Oct 13, 2022 (156)
10	1000G_HIGH_COVERAGE	ss5266326268	Oct 13, 2022 (156)
11	1000G_HIGH_COVERAGE	ss5266326269	Oct 13, 2022 (156)
12	HUGCELL_USP	ss5464242769	Oct 13, 2022 (156)
13	HUGCELL_USP	ss5464242770	Oct 13, 2022 (156)
14	HUGCELL_USP	ss5464242771	Oct 13, 2022 (156)
15	TOMMO_GENOMICS	ss5712028736	Oct 13, 2022 (156)
16	TOMMO_GENOMICS	ss5712028737	Oct 13, 2022 (156)
17	YY_MCH	ss5806882684	Oct 13, 2022 (156)
18	gnomAD - Genomes Submission ignored due to conflicting rows: Row 208420224 (NC_000005.10:151497939::T 550/131848) Row 208420225 (NC_000005.10:151497939::TT 173/131968) Row 208420226 (NC_000005.10:151497939:T: 1088/131816)...	-	Apr 26, 2021 (155)
19	gnomAD - Genomes Submission ignored due to conflicting rows: Row 208420224 (NC_000005.10:151497939::T 550/131848) Row 208420225 (NC_000005.10:151497939::TT 173/131968) Row 208420226 (NC_000005.10:151497939:T: 1088/131816)...	-	Apr 26, 2021 (155)
20	gnomAD - Genomes Submission ignored due to conflicting rows: Row 208420224 (NC_000005.10:151497939::T 550/131848) Row 208420225 (NC_000005.10:151497939::TT 173/131968) Row 208420226 (NC_000005.10:151497939:T: 1088/131816)...	-	Apr 26, 2021 (155)
21	gnomAD - Genomes Submission ignored due to conflicting rows: Row 208420224 (NC_000005.10:151497939::T 550/131848) Row 208420225 (NC_000005.10:151497939::TT 173/131968) Row 208420226 (NC_000005.10:151497939:T: 1088/131816)...	-	Apr 26, 2021 (155)
22	8.3KJPN Submission ignored due to conflicting rows: Row 32737331 (NC_000005.9:150877500:T: 46/16760) Row 32737332 (NC_000005.9:150877500::T 3/16760)	-	Apr 26, 2021 (155)
23	8.3KJPN Submission ignored due to conflicting rows: Row 32737331 (NC_000005.9:150877500:T: 46/16760) Row 32737332 (NC_000005.9:150877500::T 3/16760)	-	Apr 26, 2021 (155)
24	14KJPN Submission ignored due to conflicting rows: Row 45865840 (NC_000005.10:151497939:T: 48/28224) Row 45865841 (NC_000005.10:151497939::T 3/28224)	-	Oct 13, 2022 (156)
25	14KJPN Submission ignored due to conflicting rows: Row 45865840 (NC_000005.10:151497939:T: 48/28224) Row 45865841 (NC_000005.10:151497939::T 3/28224)	-	Oct 13, 2022 (156)
26	ALFA	NC_000005.10 - 151497940	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
ss4131783870	NC_000005.10:151497939:TT:	NC_000005.10:151497939:TTTTTTTTTTT… NC_000005.10:151497939:TTTTTTTTTTTTT:TTTTTTTTTTT	(self)
ss2998012978, ss5174768024	NC_000005.9:150877500:T:	NC_000005.10:151497939:TTTTTTTTTTT… NC_000005.10:151497939:TTTTTTTTTTTTT:TTTTTTTTTTTT	(self)
ss4131783869, ss5266326267, ss5464242769, ss5712028736	NC_000005.10:151497939:T:	NC_000005.10:151497939:TTTTTTTTTTT… NC_000005.10:151497939:TTTTTTTTTTTTT:TTTTTTTTTTTT	(self)
11057844913	NC_000005.10:151497939:TTTTTTTTTTT… NC_000005.10:151497939:TTTTTTTTTTTTT:TTTTTTTTTTTT	NC_000005.10:151497939:TTTTTTTTTTT… NC_000005.10:151497939:TTTTTTTTTTTTT:TTTTTTTTTTTT	(self)
ss193829977	NT_029289.12:12044280:T:	NC_000005.10:151497939:TTTTTTTTTTT… NC_000005.10:151497939:TTTTTTTTTTTTT:TTTTTTTTTTTT	(self)
ss5174768025	NC_000005.9:150877500::T	NC_000005.10:151497939:TTTTTTTTTTT… NC_000005.10:151497939:TTTTTTTTTTTTT:TTTTTTTTTTTTTT	(self)
ss4131783867, ss5266326269, ss5464242770, ss5712028737, ss5806882684	NC_000005.10:151497939::T	NC_000005.10:151497939:TTTTTTTTTTT… NC_000005.10:151497939:TTTTTTTTTTTTT:TTTTTTTTTTTTTT	(self)
11057844913	NC_000005.10:151497939:TTTTTTTTTTT… NC_000005.10:151497939:TTTTTTTTTTTTT:TTTTTTTTTTTTTT	NC_000005.10:151497939:TTTTTTTTTTT… NC_000005.10:151497939:TTTTTTTTTTTTT:TTTTTTTTTTTTTT	(self)
ss4131783868, ss5266326268, ss5464242771	NC_000005.10:151497939::TT	NC_000005.10:151497939:TTTTTTTTTTT… NC_000005.10:151497939:TTTTTTTTTTTTT:TTTTTTTTTTTTTTT	(self)
11057844913	NC_000005.10:151497939:TTTTTTTTTTT… NC_000005.10:151497939:TTTTTTTTTTTTT:TTTTTTTTTTTTTTT	NC_000005.10:151497939:TTTTTTTTTTT… NC_000005.10:151497939:TTTTTTTTTTTTT:TTTTTTTTTTTTTTT	(self)
11057844913	NC_000005.10:151497939:TTTTTTTTTTT… NC_000005.10:151497939:TTTTTTTTTTTTT:TTTTTTTTTTTTTTTT	NC_000005.10:151497939:TTTTTTTTTTT… NC_000005.10:151497939:TTTTTTTTTTTTT:TTTTTTTTTTTTTTTT	(self)
11057844913	NC_000005.10:151497939:TTTTTTTTTTT… NC_000005.10:151497939:TTTTTTTTTTTTT:TTTTTTTTTTTTTTTTT	NC_000005.10:151497939:TTTTTTTTTTT… NC_000005.10:151497939:TTTTTTTTTTTTT:TTTTTTTTTTTTTTTTT	(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 rs113166440

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
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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.

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dbSNP Short Genetic Variations

Welcome to the Reference SNP (rs) Report

Reference SNP (rs) Report

rs113166440