Name: rs41426948
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.

rs41426948

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr9:104907451 (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: A>C / A>G
Variation Type: SNV Single Nucleotide Variation
Frequency: G=0.038126 (5345/140192, GnomAD)
G=0.01912 (663/34680, ALFA)
G=0.00004 (1/28258, 14KJPN) (+ 14 more)
G=0.0412 (264/6404, 1000G_30x)
G=0.0405 (203/5008, 1000G)
G=0.0219 (98/4480, Estonian)
G=0.0176 (68/3854, ALSPAC)
G=0.0146 (54/3708, TWINSUK)
G=0.0632 (98/1550, HapMap)
G=0.016 (16/998, GoNL)
G=0.008 (5/626, Chileans)
G=0.017 (10/600, NorthernSweden)
G=0.051 (11/216, Qatari)
G=0.03 (1/40, GENOME_DK)
A=0.46 (11/24, SGDP_PRJ)
A=0.5 (1/2, Siberian)
G=0.5 (1/2, Siberian)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: ABCA1 : 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	34680	A=0.98088	C=0.00000, G=0.01912
European	Sub	27586	A=0.98289	C=0.00000, G=0.01711
African	Sub	3482	A=0.9589	C=0.0000, G=0.0411
African Others	Sub	122	A=0.934	C=0.000, G=0.066
African American	Sub	3360	A=0.9598	C=0.0000, G=0.0402
Asian	Sub	176	A=1.000	C=0.000, G=0.000
East Asian	Sub	116	A=1.000	C=0.000, G=0.000
Other Asian	Sub	60	A=1.00	C=0.00, G=0.00
Latin American 1	Sub	218	A=0.986	C=0.000, G=0.014
Latin American 2	Sub	836	A=0.995	C=0.000, G=0.005
South Asian	Sub	114	A=1.000	C=0.000, G=0.000
Other	Sub	2268	A=0.9819	C=0.0000, G=0.0181

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	140192	A=0.961874	G=0.038126
gnomAD - Genomes	European	Sub	75946	A=0.98097	G=0.01903
gnomAD - Genomes	African	Sub	42006	A=0.91596	G=0.08404
gnomAD - Genomes	American	Sub	13644	A=0.98190	G=0.01810
gnomAD - Genomes	Ashkenazi Jewish	Sub	3322	A=0.9865	G=0.0135
gnomAD - Genomes	East Asian	Sub	3128	A=0.9994	G=0.0006
gnomAD - Genomes	Other	Sub	2146	A=0.9646	G=0.0354
Allele Frequency Aggregator	Total	Global	34680	A=0.98088	C=0.00000, G=0.01912
Allele Frequency Aggregator	European	Sub	27586	A=0.98289	C=0.00000, G=0.01711
Allele Frequency Aggregator	African	Sub	3482	A=0.9589	C=0.0000, G=0.0411
Allele Frequency Aggregator	Other	Sub	2268	A=0.9819	C=0.0000, G=0.0181
Allele Frequency Aggregator	Latin American 2	Sub	836	A=0.995	C=0.000, G=0.005
Allele Frequency Aggregator	Latin American 1	Sub	218	A=0.986	C=0.000, G=0.014
Allele Frequency Aggregator	Asian	Sub	176	A=1.000	C=0.000, G=0.000
Allele Frequency Aggregator	South Asian	Sub	114	A=1.000	C=0.000, G=0.000
14KJPN	JAPANESE	Study-wide	28258	A=0.99996	G=0.00004
1000Genomes_30x	Global	Study-wide	6404	A=0.9588	G=0.0412
1000Genomes_30x	African	Sub	1786	A=0.9071	G=0.0929
1000Genomes_30x	Europe	Sub	1266	A=0.9866	G=0.0134
1000Genomes_30x	South Asian	Sub	1202	A=0.9534	G=0.0466
1000Genomes_30x	East Asian	Sub	1170	A=0.9983	G=0.0017
1000Genomes_30x	American	Sub	980	A=0.977	G=0.023
1000Genomes	Global	Study-wide	5008	A=0.9595	G=0.0405
1000Genomes	African	Sub	1322	A=0.9054	G=0.0946
1000Genomes	East Asian	Sub	1008	A=0.9980	G=0.0020
1000Genomes	Europe	Sub	1006	A=0.9841	G=0.0159
1000Genomes	South Asian	Sub	978	A=0.955	G=0.045
1000Genomes	American	Sub	694	A=0.977	G=0.023
Genetic variation in the Estonian population	Estonian	Study-wide	4480	A=0.9781	G=0.0219
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	A=0.9824	G=0.0176
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	A=0.9854	G=0.0146
HapMap	Global	Study-wide	1550	A=0.9368	G=0.0632
HapMap	African	Sub	692	A=0.884	G=0.116
HapMap	American	Sub	600	A=0.975	G=0.025
HapMap	Europe	Sub	176	A=0.983	G=0.017
HapMap	Asian	Sub	82	A=1.00	G=0.00
Genome of the Netherlands Release 5	Genome of the Netherlands	Study-wide	998	A=0.984	G=0.016
Chileans	Chilean	Study-wide	626	A=0.992	G=0.008
Northern Sweden	ACPOP	Study-wide	600	A=0.983	G=0.017
Qatari	Global	Study-wide	216	A=0.949	G=0.051
The Danish reference pan genome	Danish	Study-wide	40	A=0.97	G=0.03
SGDP_PRJ	Global	Study-wide	24	A=0.46	G=0.54
Siberian	Global	Study-wide	2	A=0.5	G=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 9	NC_000009.12:g.104907451A>C
GRCh38.p14 chr 9	NC_000009.12:g.104907451A>G
GRCh37.p13 chr 9	NC_000009.11:g.107669732A>C
GRCh37.p13 chr 9	NC_000009.11:g.107669732A>G
ABCA1 RefSeqGene (LRG_542)	NG_007981.1:g.25705T>G
ABCA1 RefSeqGene (LRG_542)	NG_007981.1:g.25705T>C

Gene: ABCA1, ATP binding cassette subfamily A member 1 (minus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
ABCA1 transcript	NM_005502.4:c.-92-3680T>G	N/A	Intron 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	A=	C	G
GRCh38.p14 chr 9	NC_000009.12:g.104907451=	NC_000009.12:g.104907451A>C	NC_000009.12:g.104907451A>G
GRCh37.p13 chr 9	NC_000009.11:g.107669732=	NC_000009.11:g.107669732A>C	NC_000009.11:g.107669732A>G
ABCA1 RefSeqGene (LRG_542)	NG_007981.1:g.25705=	NG_007981.1:g.25705T>G	NG_007981.1:g.25705T>C
ABCA1 transcript	NM_005502.3:c.-92-3680=	NM_005502.3:c.-92-3680T>G	NM_005502.3:c.-92-3680T>C
ABCA1 transcript	NM_005502.4:c.-92-3680=	NM_005502.4:c.-92-3680T>G	NM_005502.4:c.-92-3680T>C
ABCA1 transcript variant X4	XM_005251773.1:c.-92-3680=	XM_005251773.1:c.-92-3680T>G	XM_005251773.1:c.-92-3680T>C
ABCA1 transcript variant X5	XM_005251776.1:c.-114-18256=	XM_005251776.1:c.-114-18256T>G	XM_005251776.1:c.-114-18256T>C
ABCA1 transcript variant X5	XM_005251777.1:c.-92-3680=	XM_005251777.1:c.-92-3680T>G	XM_005251777.1:c.-92-3680T>C
ABCA1 transcript variant X6	XM_005251778.1:c.-92-3680=	XM_005251778.1:c.-92-3680T>G	XM_005251778.1:c.-92-3680T>C
ABCA1 transcript variant X8	XM_005251780.1:c.-92-3680=	XM_005251780.1:c.-92-3680T>G	XM_005251780.1:c.-92-3680T>C

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#.

52 SubSNP, 18 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	AFFY	ss66050556	Nov 30, 2006 (127)
2	AFFY	ss75955123	Dec 07, 2007 (130)
3	AFFY_GWHS	ss77100594	Dec 07, 2007 (130)
4	AFFY	ss169637998	Jul 04, 2010 (132)
5	1000GENOMES	ss224382605	Jul 14, 2010 (132)
6	ILLUMINA	ss410880400	Sep 17, 2011 (135)
7	ILLUMINA	ss481615181	May 04, 2012 (137)
8	ILLUMINA	ss485699295	May 04, 2012 (137)
9	ILLUMINA	ss534334010	Sep 08, 2015 (146)
10	TISHKOFF	ss561546972	Apr 25, 2013 (138)
11	ILLUMINA	ss779892315	Aug 21, 2014 (142)
12	ILLUMINA	ss781525769	Aug 21, 2014 (142)
13	ILLUMINA	ss835369992	Aug 21, 2014 (142)
14	EVA-GONL	ss986839961	Aug 21, 2014 (142)
15	1000GENOMES	ss1334927103	Aug 21, 2014 (142)
16	EVA_GENOME_DK	ss1583204705	Apr 01, 2015 (144)
17	EVA_DECODE	ss1596476646	Apr 01, 2015 (144)
18	EVA_UK10K_ALSPAC	ss1623276026	Apr 01, 2015 (144)
19	EVA_UK10K_TWINSUK	ss1666270059	Apr 01, 2015 (144)
20	EVA_SVP	ss1713129326	Apr 01, 2015 (144)
21	HAMMER_LAB	ss1806101808	Sep 08, 2015 (146)
22	WEILL_CORNELL_DGM	ss1930155227	Feb 12, 2016 (147)
23	JJLAB	ss2025796166	Sep 14, 2016 (149)
24	USC_VALOUEV	ss2154024843	Dec 20, 2016 (150)
25	HUMAN_LONGEVITY	ss2313328471	Dec 20, 2016 (150)
26	ILLUMINA	ss2634898837	Nov 08, 2017 (151)
27	GNOMAD	ss2881716694	Nov 08, 2017 (151)
28	SWEGEN	ss3005375816	Nov 08, 2017 (151)
29	ILLUMINA	ss3630323431	Oct 12, 2018 (152)
30	ILLUMINA	ss3632789222	Oct 12, 2018 (152)
31	ILLUMINA	ss3642703038	Oct 12, 2018 (152)
32	EGCUT_WGS	ss3672912536	Jul 13, 2019 (153)
33	EVA_DECODE	ss3724489197	Jul 13, 2019 (153)
34	ACPOP	ss3736759884	Jul 13, 2019 (153)
35	EVA	ss3769524404	Jul 13, 2019 (153)
36	KHV_HUMAN_GENOMES	ss3812692525	Jul 13, 2019 (153)
37	SGDP_PRJ	ss3872796414	Apr 26, 2020 (154)
38	TOPMED	ss4830998417	Apr 26, 2021 (155)
39	TOPMED	ss4830998418	Apr 26, 2021 (155)
40	1000G_HIGH_COVERAGE	ss5281717537	Oct 13, 2022 (156)
41	EVA	ss5389402687	Oct 13, 2022 (156)
42	HUGCELL_USP	ss5477627594	Oct 13, 2022 (156)
43	EVA	ss5509804554	Oct 13, 2022 (156)
44	1000G_HIGH_COVERAGE	ss5574547457	Oct 13, 2022 (156)
45	SANFORD_IMAGENETICS	ss5624726427	Oct 13, 2022 (156)
46	SANFORD_IMAGENETICS	ss5648004588	Oct 13, 2022 (156)
47	TOMMO_GENOMICS	ss5739047721	Oct 13, 2022 (156)
48	EVA	ss5829565495	Oct 13, 2022 (156)
49	EVA	ss5847360621	Oct 13, 2022 (156)
50	EVA	ss5917489675	Oct 13, 2022 (156)
51	EVA	ss5977199553	Oct 13, 2022 (156)
52	EVA	ss5979901503	Oct 13, 2022 (156)
53	1000Genomes	NC_000009.11 - 107669732	Oct 12, 2018 (152)
54	1000Genomes_30x	NC_000009.12 - 104907451	Oct 13, 2022 (156)
55	The Avon Longitudinal Study of Parents and Children	NC_000009.11 - 107669732	Oct 12, 2018 (152)
56	Chileans	NC_000009.11 - 107669732	Apr 26, 2020 (154)
57	Genetic variation in the Estonian population	NC_000009.11 - 107669732	Oct 12, 2018 (152)
58	The Danish reference pan genome	NC_000009.11 - 107669732	Apr 26, 2020 (154)
59	gnomAD - Genomes	NC_000009.12 - 104907451	Apr 26, 2021 (155)
60	Genome of the Netherlands Release 5	NC_000009.11 - 107669732	Apr 26, 2020 (154)
61	HapMap	NC_000009.12 - 104907451	Apr 26, 2020 (154)
62	Northern Sweden	NC_000009.11 - 107669732	Jul 13, 2019 (153)
63	Qatari	NC_000009.11 - 107669732	Apr 26, 2020 (154)
64	SGDP_PRJ	NC_000009.11 - 107669732	Apr 26, 2020 (154)
65	Siberian	NC_000009.11 - 107669732	Apr 26, 2020 (154)
66	14KJPN	NC_000009.12 - 104907451	Oct 13, 2022 (156)
67	TopMed Submission ignored due to conflicting rows: Row 668375978 (NC_000009.12:104907450:A:C 1/264690) Row 668375979 (NC_000009.12:104907450:A:G 10135/264690)	-	Apr 26, 2021 (155)
68	TopMed Submission ignored due to conflicting rows: Row 668375978 (NC_000009.12:104907450:A:C 1/264690) Row 668375979 (NC_000009.12:104907450:A:G 10135/264690)	-	Apr 26, 2021 (155)
69	UK 10K study - Twins	NC_000009.11 - 107669732	Oct 12, 2018 (152)
70	ALFA	NC_000009.12 - 104907451	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).

Associated ID	History Updated (Build)
rs56088734	May 25, 2008 (130)

Added to this RefSNP Cluster:

Submission IDs	Observation SPDI	Canonical SPDI	Source RSIDs
10567290833, ss4830998417	NC_000009.12:104907450:A:C	NC_000009.12:104907450:A:C	(self)
ss66050556, ss75955123, ss169637998, ss410880400, ss485699295, ss1596476646, ss1713129326	NC_000009.10:106709552:A:G	NC_000009.12:104907450:A:G	(self)
47226064, 26232785, 466613, 18650784, 9369642, 11708953, 10044749, 12197157, 24813394, 6541197, 26232785, ss224382605, ss481615181, ss534334010, ss561546972, ss779892315, ss781525769, ss835369992, ss986839961, ss1334927103, ss1583204705, ss1623276026, ss1666270059, ss1806101808, ss1930155227, ss2025796166, ss2154024843, ss2634898837, ss2881716694, ss3005375816, ss3630323431, ss3632789222, ss3642703038, ss3672912536, ss3736759884, ss3769524404, ss3872796414, ss5389402687, ss5509804554, ss5624726427, ss5648004588, ss5829565495, ss5847360621, ss5977199553, ss5979901503	NC_000009.11:107669731:A:G	NC_000009.12:104907450:A:G	(self)
62073392, 333830813, 3887524, 72884825, 10567290833, ss2313328471, ss3724489197, ss3812692525, ss4830998418, ss5281717537, ss5477627594, ss5574547457, ss5739047721, ss5917489675	NC_000009.12:104907450:A:G	NC_000009.12:104907450:A:G	(self)
ss77100594	NT_008470.19:36834263:A:G	NC_000009.12:104907450:A:G	(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 rs41426948

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

rs41426948