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dbSNP Short Genetic Variations

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.

rs184565478

Current Build 153

Released July 9, 2019

Organism
Homo sapiens
Position
chr5:78065571 (GRCh38.p12) 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 / G>C
Variation Type
SNV Single Nucleotide Variation
Frequency
A=0.00071 (89/125568, TOPMED)
A=0.0021 (66/31366, GnomAD)
A=0.006 (25/4480, Estonian) (+ 3 more)
A=0.002 (6/3854, ALSPAC)
A=0.001 (2/3708, TWINSUK)
A=0.01 (5/600, NorthernSweden)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
AP3B1 : Intron Variant
Publications
0 citations
Genomic View
See rs on genome
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.p12 chr 5 NC_000005.10:g.78065571G>A
GRCh38.p12 chr 5 NC_000005.10:g.78065571G>C
GRCh37.p13 chr 5 NC_000005.9:g.77361395G>A
GRCh37.p13 chr 5 NC_000005.9:g.77361395G>C
AP3B1 RefSeqGene (LRG_170) NG_007268.1:g.234134C>T
AP3B1 RefSeqGene (LRG_170) NG_007268.1:g.234134C>G
Gene: AP3B1, adaptor related protein complex 3 subunit beta 1 (minus strand)
Molecule type Change Amino acid[Codon] SO Term
AP3B1 transcript variant 2 NM_001271769.2:c. N/A Intron Variant
AP3B1 transcript variant 1 NM_003664.4:c. N/A Intron Variant
AP3B1 transcript variant X1 XM_005248618.4:c. N/A Intron Variant
AP3B1 transcript variant X2 XM_017010001.1:c. N/A Intron Variant
AP3B1 transcript variant X3 XM_005248619.5:c. N/A Genic Downstream Transcript 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

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 125568 G=0.99929 A=0.00071
gnomAD - Genomes Global Study-wide 31366 G=0.9979 A=0.0021
gnomAD - Genomes European Sub 18882 G=0.9969 A=0.0031
gnomAD - Genomes African Sub 8700 G=0.999 A=0.001
gnomAD - Genomes East Asian Sub 1558 G=1.000 A=0.000
gnomAD - Genomes Other Sub 1088 G=0.997 A=0.003
gnomAD - Genomes American Sub 848 G=1.00 A=0.00
gnomAD - Genomes Ashkenazi Jewish Sub 290 G=1.00 A=0.00
Genetic variation in the Estonian population Estonian Study-wide 4480 G=0.994 A=0.006
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 G=0.998 A=0.002
UK 10K study - Twins TWIN COHORT Study-wide 3708 G=0.999 A=0.001
Northern Sweden ACPOP Study-wide 600 G=0.99 A=0.01
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 C Note
GRCh38.p12 chr 5 NC_000005.10:g.78...

NC_000005.10:g.78065571=

NC_000005.10:g.78...

NC_000005.10:g.78065571G>A

NC_000005.10:g.78...

NC_000005.10:g.78065571G>C

GRCh37.p13 chr 5 NC_000005.9:g.773...

NC_000005.9:g.77361395=

NC_000005.9:g.773...

NC_000005.9:g.77361395G>A

NC_000005.9:g.773...

NC_000005.9:g.77361395G>C

AP3B1 RefSeqGene (LRG_170) NG_007268.1:g.234...

NG_007268.1:g.234134=

NG_007268.1:g.234...

NG_007268.1:g.234134C>T

NG_007268.1:g.234...

NG_007268.1:g.234134C>G

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#.

13 SubSNP, 6 Frequency submissions
No Submitter Submission ID Date (Build)
1 1000GENOMES ss458119335 Sep 17, 2011 (135)
2 EVA_DECODE ss1591240411 Apr 01, 2015 (144)
3 EVA_UK10K_ALSPAC ss1613200169 Apr 01, 2015 (144)
4 EVA_UK10K_TWINSUK ss1656194202 Apr 01, 2015 (144)
5 HUMAN_LONGEVITY ss2274916896 Dec 20, 2016 (150)
6 TOPMED ss2443151447 Dec 20, 2016 (150)
7 GNOMAD ss2826334026 Nov 08, 2017 (151)
8 SWEGEN ss2997177342 Nov 08, 2017 (151)
9 TOPMED ss3468443737 Nov 08, 2017 (151)
10 EGCUT_WGS ss3665056374 Jul 13, 2019 (153)
11 EVA_DECODE ss3714969055 Jul 13, 2019 (153)
12 ACPOP ss3732484100 Jul 13, 2019 (153)
13 EVA ss3763607584 Jul 13, 2019 (153)
14 The Avon Longitudinal Study of Parents and Children NC_000005.9 - 77361395 Oct 12, 2018 (152)
15 Genetic variation in the Estonian population NC_000005.9 - 77361395 Oct 12, 2018 (152)
16 gnomAD - Genomes NC_000005.9 - 77361395 Jul 13, 2019 (153)
17 Northern Sweden NC_000005.9 - 77361395 Jul 13, 2019 (153)
18 TopMed NC_000005.10 - 78065571 Oct 12, 2018 (152)
19 UK 10K study - Twins NC_000005.9 - 77361395 Oct 12, 2018 (152)
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
ss1591240411 NC_000005.8:77397150:G:A NC_000005.10:78065570:G:A (self)
15182789, 10794622, 74617744, 5768965, 15182789, ss1613200169, ss1656194202, ss2443151447, ss2826334026, ss2997177342, ss3665056374, ss3732484100 NC_000005.9:77361394:G:A NC_000005.10:78065570:G:A (self)
314166678, ss2274916896, ss3468443737, ss3714969055 NC_000005.10:78065570:G:A NC_000005.10:78065570:G:A (self)
ss458119335, ss3763607584 NC_000005.9:77361394:G:C NC_000005.10:78065570:G:C (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 rs184565478

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.post246+3cda961