Name: rs149026539
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.

rs149026539

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr1:154916577 (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: C>A / C>T
Variation Type: SNV Single Nucleotide Variation
Frequency: T=0.02410 (831/34476, ALFA)
T=0.0108 (69/6404, 1000G_30x)
T=0.0108 (54/5008, 1000G) (+ 11 more)
T=0.0496 (222/4480, Estonian)
T=0.0340 (131/3854, ALSPAC)
T=0.0383 (142/3708, TWINSUK)
T=0.029 (29/998, GoNL)
T=0.028 (17/600, NorthernSweden)
T=0.009 (2/216, Qatari)
T=0.05 (2/40, GENOME_DK)
C=0.5 (2/4, SGDP_PRJ)
T=0.5 (2/4, SGDP_PRJ)
C=0.5 (2/4, Siberian)
T=0.5 (2/4, Siberian)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: LOC105371449 : 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	34476	C=0.97590	A=0.00000, T=0.02410
European	Sub	29682	C=0.97224	A=0.00000, T=0.02776
African	Sub	2902	C=1.0000	A=0.0000, T=0.0000
African Others	Sub	114	C=1.000	A=0.000, T=0.000
African American	Sub	2788	C=1.0000	A=0.0000, T=0.0000
Asian	Sub	156	C=1.000	A=0.000, T=0.000
East Asian	Sub	130	C=1.000	A=0.000, T=0.000
Other Asian	Sub	26	C=1.00	A=0.00, T=0.00
Latin American 1	Sub	138	C=1.000	A=0.000, T=0.000
Latin American 2	Sub	600	C=1.000	A=0.000, T=0.000
South Asian	Sub	98	C=1.00	A=0.00, T=0.00
Other	Sub	900	C=0.992	A=0.000, T=0.008

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
Allele Frequency Aggregator	Total	Global	34476	C=0.97590	A=0.00000, T=0.02410
Allele Frequency Aggregator	European	Sub	29682	C=0.97224	A=0.00000, T=0.02776
Allele Frequency Aggregator	African	Sub	2902	C=1.0000	A=0.0000, T=0.0000
Allele Frequency Aggregator	Other	Sub	900	C=0.992	A=0.000, T=0.008
Allele Frequency Aggregator	Latin American 2	Sub	600	C=1.000	A=0.000, T=0.000
Allele Frequency Aggregator	Asian	Sub	156	C=1.000	A=0.000, T=0.000
Allele Frequency Aggregator	Latin American 1	Sub	138	C=1.000	A=0.000, T=0.000
Allele Frequency Aggregator	South Asian	Sub	98	C=1.00	A=0.00, T=0.00
1000Genomes_30x	Global	Study-wide	6404	C=0.9892	T=0.0108
1000Genomes_30x	African	Sub	1786	C=0.9994	T=0.0006
1000Genomes_30x	Europe	Sub	1266	C=0.9605	T=0.0395
1000Genomes_30x	South Asian	Sub	1202	C=0.9975	T=0.0025
1000Genomes_30x	East Asian	Sub	1170	C=1.0000	T=0.0000
1000Genomes_30x	American	Sub	980	C=0.985	T=0.015
1000Genomes	Global	Study-wide	5008	C=0.9892	T=0.0108
1000Genomes	African	Sub	1322	C=0.9992	T=0.0008
1000Genomes	East Asian	Sub	1008	C=1.0000	T=0.0000
1000Genomes	Europe	Sub	1006	C=0.9612	T=0.0388
1000Genomes	South Asian	Sub	978	C=0.997	T=0.003
1000Genomes	American	Sub	694	C=0.984	T=0.016
Genetic variation in the Estonian population	Estonian	Study-wide	4480	C=0.9504	T=0.0496
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	C=0.9660	T=0.0340
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	C=0.9617	T=0.0383
Genome of the Netherlands Release 5	Genome of the Netherlands	Study-wide	998	C=0.971	T=0.029
Northern Sweden	ACPOP	Study-wide	600	C=0.972	T=0.028
Qatari	Global	Study-wide	216	C=0.991	T=0.009
The Danish reference pan genome	Danish	Study-wide	40	C=0.95	T=0.05
SGDP_PRJ	Global	Study-wide	4	C=0.5	T=0.5
Siberian	Global	Study-wide	4	C=0.5	T=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 1	NC_000001.11:g.154916577C>A
GRCh38.p14 chr 1	NC_000001.11:g.154916577C>T
GRCh37.p13 chr 1	NC_000001.10:g.154889053C>A
GRCh37.p13 chr 1	NC_000001.10:g.154889053C>T

Gene: LOC105371449, uncharacterized LOC105371449 (minus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
LOC105371449 transcript	XR_001738239.2:n.	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	C=	A	T
GRCh38.p14 chr 1	NC_000001.11:g.154916577=	NC_000001.11:g.154916577C>A	NC_000001.11:g.154916577C>T
GRCh37.p13 chr 1	NC_000001.10:g.154889053=	NC_000001.10:g.154889053C>A	NC_000001.10:g.154889053C>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#.

29 SubSNP, 16 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	1000GENOMES	ss328952158	May 09, 2011 (134)
2	EVA-GONL	ss975684812	Aug 21, 2014 (142)
3	1000GENOMES	ss1292934438	Aug 21, 2014 (142)
4	EVA_GENOME_DK	ss1574393576	Apr 01, 2015 (144)
5	EVA_DECODE	ss1585066408	Apr 01, 2015 (144)
6	EVA_UK10K_ALSPAC	ss1601218987	Apr 01, 2015 (144)
7	EVA_UK10K_TWINSUK	ss1644213020	Apr 01, 2015 (144)
8	WEILL_CORNELL_DGM	ss1918918875	Feb 12, 2016 (147)
9	JJLAB	ss2019974955	Sep 14, 2016 (149)
10	USC_VALOUEV	ss2147999578	Dec 20, 2016 (150)
11	HUMAN_LONGEVITY	ss2166560455	Dec 20, 2016 (150)
12	ILLUMINA	ss2710682875	Nov 08, 2017 (151)
13	GNOMAD	ss2761341685	Nov 08, 2017 (151)
14	SWEGEN	ss2987755614	Nov 08, 2017 (151)
15	CSHL	ss3343711640	Nov 08, 2017 (151)
16	EGCUT_WGS	ss3655696066	Jul 12, 2019 (153)
17	EVA_DECODE	ss3687787074	Jul 12, 2019 (153)
18	ACPOP	ss3727487565	Jul 12, 2019 (153)
19	SGDP_PRJ	ss3850011085	Apr 25, 2020 (154)
20	TOPMED	ss4468382373	Apr 25, 2021 (155)
21	TOPMED	ss4468382374	Apr 25, 2021 (155)
22	1000G_HIGH_COVERAGE	ss5244300713	Oct 12, 2022 (156)
23	EVA	ss5322064438	Oct 12, 2022 (156)
24	HUGCELL_USP	ss5444893454	Oct 12, 2022 (156)
25	1000G_HIGH_COVERAGE	ss5517632810	Oct 12, 2022 (156)
26	SANFORD_IMAGENETICS	ss5626595778	Oct 12, 2022 (156)
27	EVA	ss5832668516	Oct 12, 2022 (156)
28	EVA	ss5910254671	Oct 12, 2022 (156)
29	EVA	ss5938389831	Oct 12, 2022 (156)
30	1000Genomes	NC_000001.10 - 154889053	Oct 11, 2018 (152)
31	1000Genomes_30x	NC_000001.11 - 154916577	Oct 12, 2022 (156)
32	The Avon Longitudinal Study of Parents and Children	NC_000001.10 - 154889053	Oct 11, 2018 (152)
33	Genetic variation in the Estonian population	NC_000001.10 - 154889053	Oct 11, 2018 (152)
34	The Danish reference pan genome	NC_000001.10 - 154889053	Apr 25, 2020 (154)
35	gnomAD - Genomes Submission ignored due to conflicting rows: Row 27116887 (NC_000001.11:154916576:C:A 1/140170) Row 27116888 (NC_000001.11:154916576:C:T 4015/140162)	-	Apr 25, 2021 (155)
36	gnomAD - Genomes Submission ignored due to conflicting rows: Row 27116887 (NC_000001.11:154916576:C:A 1/140170) Row 27116888 (NC_000001.11:154916576:C:T 4015/140162)	-	Apr 25, 2021 (155)
37	Genome of the Netherlands Release 5	NC_000001.10 - 154889053	Apr 25, 2020 (154)
38	Northern Sweden	NC_000001.10 - 154889053	Jul 12, 2019 (153)
39	Qatari	NC_000001.10 - 154889053	Apr 25, 2020 (154)
40	SGDP_PRJ	NC_000001.10 - 154889053	Apr 25, 2020 (154)
41	Siberian	NC_000001.10 - 154889053	Apr 25, 2020 (154)
42	TopMed Submission ignored due to conflicting rows: Row 31988708 (NC_000001.11:154916576:C:A 2/264690) Row 31988709 (NC_000001.11:154916576:C:T 6218/264690)	-	Apr 25, 2021 (155)
43	TopMed Submission ignored due to conflicting rows: Row 31988708 (NC_000001.11:154916576:C:A 2/264690) Row 31988709 (NC_000001.11:154916576:C:T 6218/264690)	-	Apr 25, 2021 (155)
44	UK 10K study - Twins	NC_000001.10 - 154889053	Oct 11, 2018 (152)
45	ALFA	NC_000001.11 - 154916577	Apr 25, 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
9163810107, ss4468382373	NC_000001.11:154916576:C:A	NC_000001.11:154916576:C:A	(self)
ss1585066408	NC_000001.9:153155676:C:T	NC_000001.11:154916576:C:T	(self)
3726786, 2026744, 1434314, 1709564, 880365, 772430, 960805, 2028065, 515932, 2026744, ss328952158, ss975684812, ss1292934438, ss1574393576, ss1601218987, ss1644213020, ss1918918875, ss2019974955, ss2147999578, ss2710682875, ss2761341685, ss2987755614, ss3343711640, ss3655696066, ss3727487565, ss3850011085, ss5322064438, ss5626595778, ss5832668516, ss5938389831	NC_000001.10:154889052:C:T	NC_000001.11:154916576:C:T	(self)
5158745, 9163810107, ss2166560455, ss3687787074, ss4468382374, ss5244300713, ss5444893454, ss5517632810, ss5910254671	NC_000001.11:154916576:C:T	NC_000001.11:154916576:C:T	(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 rs149026539

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.

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dbSNP Short Genetic Variations

Welcome to the Reference SNP (rs) Report

Reference SNP (rs) Report

rs149026539