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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.

rs145175062

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr4:146275670 (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
G>A
Variation Type
SNV Single Nucleotide Variation
Frequency
A=0.003971 (1051/264690, TOPMED)
A=0.003260 (457/140170, GnomAD)
A=0.00305 (44/14420, ALFA) (+ 3 more)
A=0.0045 (29/6404, 1000G_30x)
A=0.0042 (21/5008, 1000G)
A=0.005 (3/600, NorthernSweden)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
SLC10A7 : 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: 20230706150541
Population Group Sample Size Ref Allele Alt Allele
Total Global 14420 G=0.99695 A=0.00305
European Sub 9824 G=0.9998 A=0.0002
African Sub 2946 G=0.9868 A=0.0132
African Others Sub 114 G=1.000 A=0.000
African American Sub 2832 G=0.9862 A=0.0138
Asian Sub 112 G=1.000 A=0.000
East Asian Sub 86 G=1.00 A=0.00
Other Asian Sub 26 G=1.00 A=0.00
Latin American 1 Sub 146 G=1.000 A=0.000
Latin American 2 Sub 610 G=0.995 A=0.005
South Asian Sub 98 G=1.00 A=0.00
Other Sub 684 G=1.000 A=0.000


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 G=0.996029 A=0.003971
gnomAD - Genomes Global Study-wide 140170 G=0.996740 A=0.003260
gnomAD - Genomes European Sub 75902 G=0.99987 A=0.00013
gnomAD - Genomes African Sub 42022 G=0.99010 A=0.00990
gnomAD - Genomes American Sub 13642 G=0.99824 A=0.00176
gnomAD - Genomes Ashkenazi Jewish Sub 3324 G=1.0000 A=0.0000
gnomAD - Genomes East Asian Sub 3130 G=1.0000 A=0.0000
gnomAD - Genomes Other Sub 2150 G=0.9967 A=0.0033
Allele Frequency Aggregator Total Global 14420 G=0.99695 A=0.00305
Allele Frequency Aggregator European Sub 9824 G=0.9998 A=0.0002
Allele Frequency Aggregator African Sub 2946 G=0.9868 A=0.0132
Allele Frequency Aggregator Other Sub 684 G=1.000 A=0.000
Allele Frequency Aggregator Latin American 2 Sub 610 G=0.995 A=0.005
Allele Frequency Aggregator Latin American 1 Sub 146 G=1.000 A=0.000
Allele Frequency Aggregator Asian Sub 112 G=1.000 A=0.000
Allele Frequency Aggregator South Asian Sub 98 G=1.00 A=0.00
1000Genomes_30x Global Study-wide 6404 G=0.9955 A=0.0045
1000Genomes_30x African Sub 1786 G=0.9860 A=0.0140
1000Genomes_30x Europe Sub 1266 G=0.9992 A=0.0008
1000Genomes_30x South Asian Sub 1202 G=1.0000 A=0.0000
1000Genomes_30x East Asian Sub 1170 G=1.0000 A=0.0000
1000Genomes_30x American Sub 980 G=0.997 A=0.003
1000Genomes Global Study-wide 5008 G=0.9958 A=0.0042
1000Genomes African Sub 1322 G=0.9864 A=0.0136
1000Genomes East Asian Sub 1008 G=1.0000 A=0.0000
1000Genomes Europe Sub 1006 G=0.9990 A=0.0010
1000Genomes South Asian Sub 978 G=1.000 A=0.000
1000Genomes American Sub 694 G=0.997 A=0.003
Northern Sweden ACPOP Study-wide 600 G=0.995 A=0.005
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 4 NC_000004.12:g.146275670G>A
GRCh37.p13 chr 4 NC_000004.11:g.147196822G>A
Gene: SLC10A7, solute carrier family 10 member 7 (minus strand)
Molecule type Change Amino acid[Codon] SO Term
SLC10A7 transcript variant 2 NM_001029998.6:c.847+7522…

NM_001029998.6:c.847+7522C>T

N/A Intron Variant
SLC10A7 transcript variant 4 NM_001300842.3:c.847+7522…

NM_001300842.3:c.847+7522C>T

N/A Intron Variant
SLC10A7 transcript variant 5 NM_001317816.2:c.808+7522…

NM_001317816.2:c.808+7522C>T

N/A Intron Variant
SLC10A7 transcript variant 6 NM_001317817.2:c. N/A Genic Downstream Transcript Variant
SLC10A7 transcript variant 7 NM_001317818.2:c. N/A Genic Downstream Transcript Variant
SLC10A7 transcript variant 3 NM_032128.5:c. N/A Genic Downstream Transcript Variant
SLC10A7 transcript variant 1 NR_133924.2:n. N/A Intron Variant
SLC10A7 transcript variant X2 XM_011532311.3:c.808+7522…

XM_011532311.3:c.808+7522C>T

N/A Intron Variant
SLC10A7 transcript variant X5 XM_011532313.3:c.508+7522…

XM_011532313.3:c.508+7522C>T

N/A Intron Variant
SLC10A7 transcript variant X6 XM_047416248.1:c.379+7522…

XM_047416248.1:c.379+7522C>T

N/A Intron Variant
SLC10A7 transcript variant X7 XM_017008689.2:c. N/A Genic Downstream Transcript Variant
SLC10A7 transcript variant X8 XM_017008690.3:c. N/A Genic Downstream Transcript Variant
SLC10A7 transcript variant X9 XM_017008691.3:c. N/A Genic Downstream Transcript Variant
SLC10A7 transcript variant X11 XM_017008692.2:c. N/A Genic Downstream Transcript Variant
SLC10A7 transcript variant X10 XM_047416249.1:c. N/A Genic Downstream Transcript Variant
SLC10A7 transcript variant X3 XR_001741332.3:n. N/A Intron Variant
SLC10A7 transcript variant X4 XR_007057973.1:n. N/A Intron Variant
SLC10A7 transcript variant X1 XR_938780.4:n. N/A Intron 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 G= A
GRCh38.p14 chr 4 NC_000004.12:g.146275670= NC_000004.12:g.146275670G>A
GRCh37.p13 chr 4 NC_000004.11:g.147196822= NC_000004.11:g.147196822G>A
SLC10A7 transcript variant 2 NM_001029998.3:c.847+7522= NM_001029998.3:c.847+7522C>T
SLC10A7 transcript variant 2 NM_001029998.6:c.847+7522= NM_001029998.6:c.847+7522C>T
SLC10A7 transcript variant 4 NM_001300842.3:c.847+7522= NM_001300842.3:c.847+7522C>T
SLC10A7 transcript variant 5 NM_001317816.2:c.808+7522= NM_001317816.2:c.808+7522C>T
SLC10A7 transcript variant X1 XM_005263276.1:c.847+7522= XM_005263276.1:c.847+7522C>T
SLC10A7 transcript variant X2 XM_005263277.1:c.808+7522= XM_005263277.1:c.808+7522C>T
SLC10A7 transcript variant X3 XM_005263278.1:c.808+7522= XM_005263278.1:c.808+7522C>T
SLC10A7 transcript variant X2 XM_011532311.3:c.808+7522= XM_011532311.3:c.808+7522C>T
SLC10A7 transcript variant X5 XM_011532313.3:c.508+7522= XM_011532313.3:c.508+7522C>T
SLC10A7 transcript variant X6 XM_047416248.1:c.379+7522= XM_047416248.1:c.379+7522C>T
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#.

14 SubSNP, 6 Frequency submissions
No Submitter Submission ID Date (Build)
1 1000GENOMES ss332026971 May 09, 2011 (134)
2 JMKIDD_LAB ss1072048781 Aug 21, 2014 (142)
3 1000GENOMES ss1312278952 Aug 21, 2014 (142)
4 HUMAN_LONGEVITY ss2268082114 Dec 20, 2016 (150)
5 GNOMAD ss2816592678 Nov 08, 2017 (151)
6 ACPOP ss3731708743 Jul 13, 2019 (153)
7 TOPMED ss4636054141 Apr 26, 2021 (155)
8 1000G_HIGH_COVERAGE ss5261428140 Oct 13, 2022 (156)
9 EVA ss5353035513 Oct 13, 2022 (156)
10 HUGCELL_USP ss5459939168 Oct 13, 2022 (156)
11 1000G_HIGH_COVERAGE ss5543739308 Oct 13, 2022 (156)
12 SANFORD_IMAGENETICS ss5636333588 Oct 13, 2022 (156)
13 EVA ss5865964342 Oct 13, 2022 (156)
14 EVA ss5964736427 Oct 13, 2022 (156)
15 1000Genomes NC_000004.11 - 147196822 Oct 12, 2018 (152)
16 1000Genomes_30x NC_000004.12 - 146275670 Oct 13, 2022 (156)
17 gnomAD - Genomes NC_000004.12 - 146275670 Apr 26, 2021 (155)
18 Northern Sweden NC_000004.11 - 147196822 Jul 13, 2019 (153)
19 TopMed NC_000004.12 - 146275670 Apr 26, 2021 (155)
20 ALFA NC_000004.12 - 146275670 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
23771654, 4993608, ss332026971, ss1072048781, ss1312278952, ss2816592678, ss3731708743, ss5353035513, ss5636333588, ss5964736427 NC_000004.11:147196821:G:A NC_000004.12:146275669:G:A (self)
31265243, 168370034, 473431697, 376481148, ss2268082114, ss4636054141, ss5261428140, ss5459939168, ss5543739308, ss5865964342 NC_000004.12:146275669:G:A NC_000004.12:146275669:G: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 rs145175062

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.post761+d5e8e07