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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.

rs114859019

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chrX:153731940 (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>T
Variation Type
SNV Single Nucleotide Variation
Frequency
T=0.017983 (4760/264690, TOPMED)
T=0.016118 (1681/104296, GnomAD)
T=0.01110 (156/14050, ALFA) (+ 4 more)
T=0.0202 (97/4805, 1000G_30x)
T=0.0196 (74/3775, 1000G)
T=0.009 (1/108, Qatari)
C=0.0 (0/4, SGDP_PRJ)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
ABCD1 : 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 14050 C=0.98890 T=0.01110
European Sub 9690 C=0.9998 T=0.0002
African Sub 2898 C=0.9503 T=0.0497
African Others Sub 114 C=0.965 T=0.035
African American Sub 2784 C=0.9497 T=0.0503
Asian Sub 112 C=1.000 T=0.000
East Asian Sub 86 C=1.00 T=0.00
Other Asian Sub 26 C=1.00 T=0.00
Latin American 1 Sub 146 C=0.986 T=0.014
Latin American 2 Sub 610 C=0.995 T=0.005
South Asian Sub 98 C=1.00 T=0.00
Other Sub 496 C=0.990 T=0.010


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 264690 C=0.982017 T=0.017983
gnomAD - Genomes Global Study-wide 104296 C=0.983882 T=0.016118
gnomAD - Genomes European Sub 57279 C=0.99972 T=0.00028
gnomAD - Genomes African Sub 31346 C=0.95017 T=0.04983
gnomAD - Genomes American Sub 9333 C=0.9912 T=0.0088
gnomAD - Genomes Ashkenazi Jewish Sub 2523 C=1.0000 T=0.0000
gnomAD - Genomes East Asian Sub 2241 C=1.0000 T=0.0000
gnomAD - Genomes Other Sub 1574 C=0.9867 T=0.0133
Allele Frequency Aggregator Total Global 14050 C=0.98890 T=0.01110
Allele Frequency Aggregator European Sub 9690 C=0.9998 T=0.0002
Allele Frequency Aggregator African Sub 2898 C=0.9503 T=0.0497
Allele Frequency Aggregator Latin American 2 Sub 610 C=0.995 T=0.005
Allele Frequency Aggregator Other Sub 496 C=0.990 T=0.010
Allele Frequency Aggregator Latin American 1 Sub 146 C=0.986 T=0.014
Allele Frequency Aggregator Asian Sub 112 C=1.000 T=0.000
Allele Frequency Aggregator South Asian Sub 98 C=1.00 T=0.00
1000Genomes_30x Global Study-wide 4805 C=0.9798 T=0.0202
1000Genomes_30x African Sub 1328 C=0.9315 T=0.0685
1000Genomes_30x Europe Sub 961 C=1.000 T=0.000
1000Genomes_30x South Asian Sub 883 C=1.000 T=0.000
1000Genomes_30x East Asian Sub 878 C=1.000 T=0.000
1000Genomes_30x American Sub 755 C=0.992 T=0.008
1000Genomes Global Study-wide 3775 C=0.9804 T=0.0196
1000Genomes African Sub 1003 C=0.9312 T=0.0688
1000Genomes Europe Sub 766 C=1.000 T=0.000
1000Genomes East Asian Sub 764 C=1.000 T=0.000
1000Genomes South Asian Sub 718 C=1.000 T=0.000
1000Genomes American Sub 524 C=0.990 T=0.010
Qatari Global Study-wide 108 C=0.991 T=0.009
SGDP_PRJ Global Study-wide 4 C=0.0 T=1.0
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 X NC_000023.11:g.153731940C>T
GRCh37.p13 chr X NC_000023.10:g.152997395C>T
ABCD1 RefSeqGene (LRG_1017) NG_009022.2:g.12073C>T
GRCh37.p13 chr X fix patch HG1497_PATCH NW_003871103.3:g.1165923C>T
Gene: ABCD1, ATP binding cassette subfamily D member 1 (plus strand)
Molecule type Change Amino acid[Codon] SO Term
ABCD1 transcript NM_000033.4:c.1081+2528C>T N/A Intron Variant
ABCD1 transcript variant X1 XM_047441916.1:c.1081+252…

XM_047441916.1:c.1081+2528C>T

N/A Intron Variant
ABCD1 transcript variant X2 XM_047441917.1:c.1081+252…

XM_047441917.1:c.1081+2528C>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 C= T
GRCh38.p14 chr X NC_000023.11:g.153731940= NC_000023.11:g.153731940C>T
GRCh37.p13 chr X NC_000023.10:g.152997395= NC_000023.10:g.152997395C>T
ABCD1 RefSeqGene (LRG_1017) NG_009022.2:g.12073= NG_009022.2:g.12073C>T
GRCh37.p13 chr X fix patch HG1497_PATCH NW_003871103.3:g.1165923= NW_003871103.3:g.1165923C>T
ABCD1 transcript NM_000033.3:c.1081+2528= NM_000033.3:c.1081+2528C>T
ABCD1 transcript NM_000033.4:c.1081+2528= NM_000033.4:c.1081+2528C>T
ABCD1 transcript variant X1 XM_047441916.1:c.1081+2528= XM_047441916.1:c.1081+2528C>T
ABCD1 transcript variant X2 XM_047441917.1:c.1081+2528= XM_047441917.1:c.1081+2528C>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#.

16 SubSNP, 7 Frequency submissions
No Submitter Submission ID Date (Build)
1 1000GENOMES ss212188156 Jul 14, 2010 (132)
2 1000GENOMES ss467025639 Sep 17, 2011 (135)
3 TISHKOFF ss567106491 Apr 25, 2013 (138)
4 1000GENOMES ss1556682425 Apr 09, 2015 (144)
5 WEILL_CORNELL_DGM ss1939848736 Feb 17, 2016 (147)
6 HUMAN_LONGEVITY ss2321296028 Dec 20, 2016 (150)
7 GNOMAD ss2984711164 Oct 13, 2018 (152)
8 KHV_HUMAN_GENOMES ss3823522008 Jul 14, 2019 (153)
9 SGDP_PRJ ss3892527763 Apr 27, 2020 (154)
10 GNOMAD ss4381096021 Apr 27, 2021 (155)
11 TOPMED ss5141482399 Apr 27, 2021 (155)
12 1000G_HIGH_COVERAGE ss5314351996 Oct 17, 2022 (156)
13 HUGCELL_USP ss5505705840 Oct 17, 2022 (156)
14 1000G_HIGH_COVERAGE ss5623683686 Oct 17, 2022 (156)
15 SANFORD_IMAGENETICS ss5666092376 Oct 17, 2022 (156)
16 EVA ss5979241627 Oct 17, 2022 (156)
17 1000Genomes NC_000023.10 - 152997395 Oct 13, 2018 (152)
18 1000Genomes_30x NC_000023.11 - 153731940 Oct 17, 2022 (156)
19 gnomAD - Genomes NC_000023.11 - 153731940 Apr 27, 2021 (155)
20 Qatari NC_000023.10 - 152997395 Apr 27, 2020 (154)
21 SGDP_PRJ NC_000023.10 - 152997395 Apr 27, 2020 (154)
22 TopMed NC_000023.11 - 153731940 Apr 27, 2021 (155)
23 ALFA NC_000023.11 - 153731940 Apr 27, 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
ss212188156 NC_000023.9:152650588:C:T NC_000023.11:153731939:C:T (self)
84635808, 21890658, 44544743, ss467025639, ss567106491, ss1556682425, ss1939848736, ss2984711164, ss3892527763, ss5666092376, ss5979241627 NC_000023.10:152997394:C:T NC_000023.11:153731939:C:T (self)
111209621, 594462807, 705088756, 4562561391, ss2321296028, ss3823522008, ss4381096021, ss5141482399, ss5314351996, ss5505705840, ss5623683686 NC_000023.11:153731939:C:T NC_000023.11:153731939:C:T (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 rs114859019

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.post761+d5e8e07