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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.

rs575912645

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr16:71800137 (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=0.000489 (68/139096, GnomAD)
A=0.00066 (11/16702, ALFA)
A=0.0003 (2/6404, 1000G_30x) (+ 2 more)
A=0.0002 (1/5008, 1000G)
A=0.0004 (2/4480, Estonian)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
AP1G1 : 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 Alt HMOZ HTRZ HWEP
Total Global 16702 G=0.99934 A=0.00066 0.998683 0.0 0.001317 0
European Sub 12214 G=0.99910 A=0.00090 0.998199 0.0 0.001801 0
African Sub 2864 G=1.0000 A=0.0000 1.0 0.0 0.0 N/A
African Others Sub 108 G=1.000 A=0.000 1.0 0.0 0.0 N/A
African American Sub 2756 G=1.0000 A=0.0000 1.0 0.0 0.0 N/A
Asian Sub 108 G=1.000 A=0.000 1.0 0.0 0.0 N/A
East Asian Sub 84 G=1.00 A=0.00 1.0 0.0 0.0 N/A
Other Asian Sub 24 G=1.00 A=0.00 1.0 0.0 0.0 N/A
Latin American 1 Sub 146 G=1.000 A=0.000 1.0 0.0 0.0 N/A
Latin American 2 Sub 610 G=1.000 A=0.000 1.0 0.0 0.0 N/A
South Asian Sub 94 G=1.00 A=0.00 1.0 0.0 0.0 N/A
Other Sub 666 G=1.000 A=0.000 1.0 0.0 0.0 N/A


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 - Genomes Global Study-wide 139096 G=0.999511 A=0.000489
gnomAD - Genomes European Sub 75494 G=0.99918 A=0.00082
gnomAD - Genomes African Sub 41560 G=0.99995 A=0.00005
gnomAD - Genomes American Sub 13468 G=0.99978 A=0.00022
gnomAD - Genomes Ashkenazi Jewish Sub 3324 G=1.0000 A=0.0000
gnomAD - Genomes East Asian Sub 3114 G=1.0000 A=0.0000
gnomAD - Genomes Other Sub 2136 G=0.9995 A=0.0005
Allele Frequency Aggregator Total Global 16702 G=0.99934 A=0.00066
Allele Frequency Aggregator European Sub 12214 G=0.99910 A=0.00090
Allele Frequency Aggregator African Sub 2864 G=1.0000 A=0.0000
Allele Frequency Aggregator Other Sub 666 G=1.000 A=0.000
Allele Frequency Aggregator Latin American 2 Sub 610 G=1.000 A=0.000
Allele Frequency Aggregator Latin American 1 Sub 146 G=1.000 A=0.000
Allele Frequency Aggregator Asian Sub 108 G=1.000 A=0.000
Allele Frequency Aggregator South Asian Sub 94 G=1.00 A=0.00
1000Genomes_30x Global Study-wide 6404 G=0.9997 A=0.0003
1000Genomes_30x African Sub 1786 G=0.9989 A=0.0011
1000Genomes_30x Europe Sub 1266 G=1.0000 A=0.0000
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=1.000 A=0.000
1000Genomes Global Study-wide 5008 G=0.9998 A=0.0002
1000Genomes African Sub 1322 G=0.9992 A=0.0008
1000Genomes East Asian Sub 1008 G=1.0000 A=0.0000
1000Genomes Europe Sub 1006 G=1.0000 A=0.0000
1000Genomes South Asian Sub 978 G=1.000 A=0.000
1000Genomes American Sub 694 G=1.000 A=0.000
Genetic variation in the Estonian population Estonian Study-wide 4480 G=0.9996 A=0.0004
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 16 NC_000016.10:g.71800137G>A
GRCh37.p13 chr 16 NC_000016.9:g.71834040G>A
Gene: AP1G1, adaptor related protein complex 1 subunit gamma 1 (minus strand)
Molecule type Change Amino acid[Codon] SO Term
AP1G1 transcript variant 1 NM_001030007.2:c.-4+8626C…

NM_001030007.2:c.-4+8626C>T

N/A Intron Variant
AP1G1 transcript variant 2 NM_001128.6:c.-4+8626C>T 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 16 NC_000016.10:g.71800137= NC_000016.10:g.71800137G>A
GRCh37.p13 chr 16 NC_000016.9:g.71834040= NC_000016.9:g.71834040G>A
AP1G1 transcript variant 1 NM_001030007.1:c.-4+8626= NM_001030007.1:c.-4+8626C>T
AP1G1 transcript variant 1 NM_001030007.2:c.-4+8626= NM_001030007.2:c.-4+8626C>T
AP1G1 transcript variant 2 NM_001128.5:c.-4+8626= NM_001128.5:c.-4+8626C>T
AP1G1 transcript variant 2 NM_001128.6:c.-4+8626= NM_001128.6:c.-4+8626C>T
AP1G1 transcript variant X1 XM_005255821.1:c.243+8368= XM_005255821.1:c.243+8368C>T
AP1G1 transcript variant X2 XM_005255822.1:c.243+8368= XM_005255822.1:c.243+8368C>T
AP1G1 transcript variant X3 XM_005255823.1:c.66+6549= XM_005255823.1:c.66+6549C>T
AP1G1 transcript variant X4 XM_005255824.1:c.-4+7878= XM_005255824.1:c.-4+7878C>T
AP1G1 transcript variant X5 XM_005255825.1:c.-4+7878= XM_005255825.1:c.-4+7878C>T
AP1G1 transcript variant X6 XM_005255826.1:c.-4+7664= XM_005255826.1:c.-4+7664C>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#.

9 SubSNP, 5 Frequency submissions
No Submitter Submission ID Date (Build)
1 1000GENOMES ss1356797267 Aug 21, 2014 (142)
2 EVA_DECODE ss1696669123 Apr 01, 2015 (144)
3 GNOMAD ss2944626420 Nov 08, 2017 (151)
4 SWEGEN ss3014741627 Nov 08, 2017 (151)
5 EGCUT_WGS ss3681717811 Jul 13, 2019 (153)
6 1000G_HIGH_COVERAGE ss5301448728 Oct 16, 2022 (156)
7 EVA ss5424615292 Oct 16, 2022 (156)
8 1000G_HIGH_COVERAGE ss5604355109 Oct 16, 2022 (156)
9 EVA ss5846598306 Oct 16, 2022 (156)
10 1000Genomes NC_000016.9 - 71834040 Oct 12, 2018 (152)
11 1000Genomes_30x NC_000016.10 - 71800137 Oct 16, 2022 (156)
12 Genetic variation in the Estonian population NC_000016.9 - 71834040 Oct 12, 2018 (152)
13 gnomAD - Genomes NC_000016.10 - 71800137 Apr 26, 2021 (155)
14 ALFA NC_000016.10 - 71800137 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
ss1696669123 NC_000016.8:70391540:G:A NC_000016.10:71800136:G:A (self)
69979802, 27456059, ss1356797267, ss2944626420, ss3014741627, ss3681717811, ss5424615292, ss5846598306 NC_000016.9:71834039:G:A NC_000016.10:71800136:G:A (self)
91881044, 493709021, 4386786521, ss5301448728, ss5604355109 NC_000016.10:71800136:G:A NC_000016.10:71800136: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 rs575912645

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