Name: rs79145585
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.

rs79145585

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr2:168993025 (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=0.006370 (1686/264690, TOPMED)
A=0.006244 (874/139968, GnomAD)
A=0.00388 (81/20868, ALFA) (+ 5 more)
A=0.0078 (50/6404, 1000G_30x)
A=0.0066 (33/5008, 1000G)
A=0.014 (3/216, Qatari)
G=0.5 (1/2, SGDP_PRJ)
A=0.5 (1/2, SGDP_PRJ)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: ABCB11 : 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	20868	G=0.99612	A=0.00388
European	Sub	15648	G=1.00000	A=0.00000
African	Sub	3076	G=0.9756	A=0.0244
African Others	Sub	118	G=0.949	A=0.051
African American	Sub	2958	G=0.9767	A=0.0233
Asian	Sub	126	G=1.000	A=0.000
East Asian	Sub	98	G=1.00	A=0.00
Other Asian	Sub	28	G=1.00	A=0.00
Latin American 1	Sub	160	G=0.994	A=0.006
Latin American 2	Sub	644	G=0.998	A=0.002
South Asian	Sub	98	G=1.00	A=0.00
Other	Sub	1116	G=0.9964	A=0.0036

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
TopMed	Global	Study-wide	264690	G=0.993630	A=0.006370
gnomAD - Genomes	Global	Study-wide	139968	G=0.993756	A=0.006244
gnomAD - Genomes	European	Sub	75850	G=0.99996	A=0.00004
gnomAD - Genomes	African	Sub	41952	G=0.98010	A=0.01990
gnomAD - Genomes	American	Sub	13586	G=0.99787	A=0.00213
gnomAD - Genomes	Ashkenazi Jewish	Sub	3324	G=1.0000	A=0.0000
gnomAD - Genomes	East Asian	Sub	3104	G=1.0000	A=0.0000
gnomAD - Genomes	Other	Sub	2152	G=0.9967	A=0.0033
Allele Frequency Aggregator	Total	Global	20868	G=0.99612	A=0.00388
Allele Frequency Aggregator	European	Sub	15648	G=1.00000	A=0.00000
Allele Frequency Aggregator	African	Sub	3076	G=0.9756	A=0.0244
Allele Frequency Aggregator	Other	Sub	1116	G=0.9964	A=0.0036
Allele Frequency Aggregator	Latin American 2	Sub	644	G=0.998	A=0.002
Allele Frequency Aggregator	Latin American 1	Sub	160	G=0.994	A=0.006
Allele Frequency Aggregator	Asian	Sub	126	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=0.9922	A=0.0078
1000Genomes_30x	African	Sub	1786	G=0.9748	A=0.0252
1000Genomes_30x	Europe	Sub	1266	G=0.9984	A=0.0016
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=0.9934	A=0.0066
1000Genomes	African	Sub	1322	G=0.9773	A=0.0227
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
Qatari	Global	Study-wide	216	G=0.986	A=0.014
SGDP_PRJ	Global	Study-wide	2	G=0.5	A=0.5

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 2	NC_000002.12:g.168993025G>A
GRCh37.p13 chr 2	NC_000002.11:g.169849535G>A
ABCB11 RefSeqGene (LRG_1199)	NG_007374.2:g.43372C>T

Gene: ABCB11, ATP binding cassette subfamily B member 11 (minus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
ABCB11 transcript	NM_003742.4:c.783+686C>T	N/A	Intron Variant
ABCB11 transcript variant X2	XM_006712817.4:c.825+686C… XM_006712817.4:c.825+686C>T	N/A	Intron Variant
ABCB11 transcript variant X1	XM_011512078.3:c.885+686C… XM_011512078.3:c.885+686C>T	N/A	Intron Variant
ABCB11 transcript variant X5	XM_011512080.3:c.885+686C… XM_011512080.3:c.885+686C>T	N/A	Intron Variant
ABCB11 transcript variant X3	XM_017005165.2:c.885+686C… XM_017005165.2:c.885+686C>T	N/A	Intron Variant
ABCB11 transcript variant X4	XM_017005166.2:c.114+686C… XM_017005166.2:c.114+686C>T	N/A	Intron Variant
ABCB11 transcript variant X6	XM_017005167.2:c.	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	G=	A
GRCh38.p14 chr 2	NC_000002.12:g.168993025=	NC_000002.12:g.168993025G>A
GRCh37.p13 chr 2	NC_000002.11:g.169849535=	NC_000002.11:g.169849535G>A
ABCB11 RefSeqGene (LRG_1199)	NG_007374.2:g.43372=	NG_007374.2:g.43372C>T
ABCB11 transcript	NM_003742.2:c.783+686=	NM_003742.2:c.783+686C>T
ABCB11 transcript	NM_003742.4:c.783+686=	NM_003742.4:c.783+686C>T
ABCB11 transcript variant X2	XM_006712817.4:c.825+686=	XM_006712817.4:c.825+686C>T
ABCB11 transcript variant X1	XM_011512078.3:c.885+686=	XM_011512078.3:c.885+686C>T
ABCB11 transcript variant X5	XM_011512080.3:c.885+686=	XM_011512080.3:c.885+686C>T
ABCB11 transcript variant X3	XM_017005165.2:c.885+686=	XM_017005165.2:c.885+686C>T
ABCB11 transcript variant X4	XM_017005166.2:c.114+686=	XM_017005166.2:c.114+686C>T

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#.

25 SubSNP, 7 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	1000GENOMES	ss219645276	Jul 14, 2010 (132)
2	ILLUMINA	ss480542823	May 04, 2012 (137)
3	ILLUMINA	ss483953119	May 04, 2012 (137)
4	ILLUMINA	ss533803441	Sep 08, 2015 (146)
5	TISHKOFF	ss556025438	Apr 25, 2013 (138)
6	ILLUMINA	ss779210210	Sep 08, 2015 (146)
7	ILLUMINA	ss781256951	Sep 08, 2015 (146)
8	ILLUMINA	ss834676021	Sep 08, 2015 (146)
9	1000GENOMES	ss1300360248	Aug 21, 2014 (142)
10	WEILL_CORNELL_DGM	ss1920878373	Feb 12, 2016 (147)
11	HUMAN_LONGEVITY	ss2236438878	Dec 20, 2016 (150)
12	ILLUMINA	ss2633702684	Nov 08, 2017 (151)
13	GNOMAD	ss2782624385	Nov 08, 2017 (151)
14	ILLUMINA	ss3628217845	Oct 11, 2018 (152)
15	ILLUMINA	ss3631664361	Oct 11, 2018 (152)
16	KHV_HUMAN_GENOMES	ss3802057954	Jul 13, 2019 (153)
17	SGDP_PRJ	ss3853938711	Apr 25, 2020 (154)
18	TOPMED	ss4533159254	Apr 26, 2021 (155)
19	1000G_HIGH_COVERAGE	ss5250909140	Oct 12, 2022 (156)
20	EVA	ss5333991679	Oct 12, 2022 (156)
21	HUGCELL_USP	ss5450633910	Oct 12, 2022 (156)
22	1000G_HIGH_COVERAGE	ss5527666811	Oct 12, 2022 (156)
23	SANFORD_IMAGENETICS	ss5630321927	Oct 12, 2022 (156)
24	EVA	ss5933411603	Oct 12, 2022 (156)
25	EVA	ss5956545208	Oct 12, 2022 (156)
26	1000Genomes	NC_000002.11 - 169849535	Oct 11, 2018 (152)
27	1000Genomes_30x	NC_000002.12 - 168993025	Oct 12, 2022 (156)
28	gnomAD - Genomes	NC_000002.12 - 168993025	Apr 26, 2021 (155)
29	Qatari	NC_000002.11 - 169849535	Apr 25, 2020 (154)
30	SGDP_PRJ	NC_000002.11 - 169849535	Apr 25, 2020 (154)
31	TopMed	NC_000002.12 - 168993025	Apr 26, 2021 (155)
32	ALFA	NC_000002.12 - 168993025	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
ss483953119	NC_000002.10:169557780:G:A	NC_000002.12:168993024:G:A	(self)
11415031, 2920303, 5955691, ss219645276, ss480542823, ss533803441, ss556025438, ss779210210, ss781256951, ss834676021, ss1300360248, ss1920878373, ss2633702684, ss2782624385, ss3628217845, ss3631664361, ss3853938711, ss5333991679, ss5630321927, ss5956545208	NC_000002.11:169849534:G:A	NC_000002.12:168993024:G:A	(self)
15192746, 81375822, 336982133, 14348645789, ss2236438878, ss3802057954, ss4533159254, ss5250909140, ss5450633910, ss5527666811, ss5933411603	NC_000002.12:168993024:G:A	NC_000002.12:168993024:G:A	(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 rs79145585

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

rs79145585