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dbSNP Short Genetic Variations

Examples: rs268, BRCA1 and more Advanced search

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.

rs144581707

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chrX:18908013 (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
T>C
Variation Type
SNV Single Nucleotide Variation
Frequency
C=0.000004 (1/264690, TOPMED)
C=0.000005 (1/183520, GnomAD_exome)
C=0.000000 (0/163664, ALFA) (+ 2 more)
C=0.000010 (1/103855, GnomAD)
C=0.00002 (2/87726, ExAC)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
PHKA2 : Missense 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 163664 T=1.000000 C=0.000000
European Sub 146760 T=1.000000 C=0.000000
African Sub 4288 T=1.0000 C=0.0000
African Others Sub 168 T=1.000 C=0.000
African American Sub 4120 T=1.0000 C=0.0000
Asian Sub 3334 T=1.0000 C=0.0000
East Asian Sub 2684 T=1.0000 C=0.0000
Other Asian Sub 650 T=1.000 C=0.000
Latin American 1 Sub 442 T=1.000 C=0.000
Latin American 2 Sub 950 T=1.000 C=0.000
South Asian Sub 280 T=1.000 C=0.000
Other Sub 7610 T=1.0000 C=0.0000


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 T=0.999996 C=0.000004
gnomAD - Exomes Global Study-wide 183520 T=0.999995 C=0.000005
gnomAD - Exomes European Sub 97964 T=0.99999 C=0.00001
gnomAD - Exomes Asian Sub 32939 T=1.00000 C=0.00000
gnomAD - Exomes American Sub 27431 T=1.00000 C=0.00000
gnomAD - Exomes African Sub 13163 T=1.00000 C=0.00000
gnomAD - Exomes Ashkenazi Jewish Sub 7489 T=1.0000 C=0.0000
gnomAD - Exomes Other Sub 4534 T=1.0000 C=0.0000
Allele Frequency Aggregator Total Global 163664 T=1.000000 C=0.000000
Allele Frequency Aggregator European Sub 146760 T=1.000000 C=0.000000
Allele Frequency Aggregator Other Sub 7610 T=1.0000 C=0.0000
Allele Frequency Aggregator African Sub 4288 T=1.0000 C=0.0000
Allele Frequency Aggregator Asian Sub 3334 T=1.0000 C=0.0000
Allele Frequency Aggregator Latin American 2 Sub 950 T=1.000 C=0.000
Allele Frequency Aggregator Latin American 1 Sub 442 T=1.000 C=0.000
Allele Frequency Aggregator South Asian Sub 280 T=1.000 C=0.000
gnomAD - Genomes Global Study-wide 103855 T=0.999990 C=0.000010
gnomAD - Genomes European Sub 57034 T=0.99998 C=0.00002
gnomAD - Genomes African Sub 31204 T=1.00000 C=0.00000
gnomAD - Genomes American Sub 9303 T=1.0000 C=0.0000
gnomAD - Genomes Ashkenazi Jewish Sub 2513 T=1.0000 C=0.0000
gnomAD - Genomes East Asian Sub 2232 T=1.0000 C=0.0000
gnomAD - Genomes Other Sub 1569 T=1.0000 C=0.0000
ExAC Global Study-wide 87726 T=0.99998 C=0.00002
ExAC Europe Sub 52506 T=0.99996 C=0.00004
ExAC Asian Sub 16756 T=1.00000 C=0.00000
ExAC American Sub 9321 T=1.0000 C=0.0000
ExAC African Sub 8512 T=1.0000 C=0.0000
ExAC Other Sub 631 T=1.000 C=0.000
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.18908013T>C
GRCh37.p13 chr X NC_000023.10:g.18926131T>C
PHKA2 RefSeqGene NG_016622.1:g.81350A>G
Gene: PHKA2, phosphorylase kinase regulatory subunit alpha 2 (minus strand)
Molecule type Change Amino acid[Codon] SO Term
PHKA2 transcript NM_000292.3:c.2404A>G T [ACC] > A [GCC] Coding Sequence Variant
phosphorylase b kinase regulatory subunit alpha, liver isoform NP_000283.1:p.Thr802Ala T (Thr) > A (Ala) Missense Variant
PHKA2 transcript variant X1 XM_006724496.5:c.2404A>G T [ACC] > A [GCC] Coding Sequence Variant
phosphorylase b kinase regulatory subunit alpha, liver isoform isoform X1 XP_006724559.1:p.Thr802Ala T (Thr) > A (Ala) Missense Variant
PHKA2 transcript variant X2 XM_005274548.6:c.2404A>G T [ACC] > A [GCC] Coding Sequence Variant
phosphorylase b kinase regulatory subunit alpha, liver isoform isoform X2 XP_005274605.1:p.Thr802Ala T (Thr) > A (Ala) Missense Variant
PHKA2 transcript variant X3 XM_011545537.4:c.2305A>G T [ACC] > A [GCC] Coding Sequence Variant
phosphorylase b kinase regulatory subunit alpha, liver isoform isoform X3 XP_011543839.1:p.Thr769Ala T (Thr) > A (Ala) Missense Variant
PHKA2 transcript variant X4 XM_005274550.6:c.2404A>G T [ACC] > A [GCC] Coding Sequence Variant
phosphorylase b kinase regulatory subunit alpha, liver isoform isoform X4 XP_005274607.1:p.Thr802Ala T (Thr) > A (Ala) Missense Variant
PHKA2 transcript variant X5 XM_047442163.1:c.2305A>G T [ACC] > A [GCC] Coding Sequence Variant
phosphorylase b kinase regulatory subunit alpha, liver isoform isoform X5 XP_047298119.1:p.Thr769Ala T (Thr) > A (Ala) Missense Variant
PHKA2 transcript variant X6 XM_047442164.1:c.2305A>G T [ACC] > A [GCC] Coding Sequence Variant
phosphorylase b kinase regulatory subunit alpha, liver isoform isoform X6 XP_047298120.1:p.Thr769Ala T (Thr) > A (Ala) Missense Variant
PHKA2 transcript variant X7 XM_047442165.1:c.2305A>G T [ACC] > A [GCC] Coding Sequence Variant
phosphorylase b kinase regulatory subunit alpha, liver isoform isoform X7 XP_047298121.1:p.Thr769Ala T (Thr) > A (Ala) Missense Variant
PHKA2 transcript variant X10 XM_047442166.1:c.1858A>G T [ACC] > A [GCC] Coding Sequence Variant
phosphorylase b kinase regulatory subunit alpha, liver isoform isoform X8 XP_047298122.1:p.Thr620Ala T (Thr) > A (Ala) Missense Variant
PHKA2 transcript variant X11 XM_017029580.3:c.1498A>G T [ACC] > A [GCC] Coding Sequence Variant
phosphorylase b kinase regulatory subunit alpha, liver isoform isoform X9 XP_016885069.1:p.Thr500Ala T (Thr) > A (Ala) Missense Variant
PHKA2 transcript variant X12 XM_011545538.4:c.1387A>G T [ACC] > A [GCC] Coding Sequence Variant
phosphorylase b kinase regulatory subunit alpha, liver isoform isoform X10 XP_011543840.1:p.Thr463Ala T (Thr) > A (Ala) Missense Variant
PHKA2 transcript variant X8 XR_950461.4:n.2586A>G N/A Non Coding Transcript Variant
PHKA2 transcript variant X9 XR_001755697.3:n.2586A>G N/A Non Coding 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

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 T= C
GRCh38.p14 chr X NC_000023.11:g.18908013= NC_000023.11:g.18908013T>C
GRCh37.p13 chr X NC_000023.10:g.18926131= NC_000023.10:g.18926131T>C
PHKA2 RefSeqGene NG_016622.1:g.81350= NG_016622.1:g.81350A>G
PHKA2 transcript NM_000292.3:c.2404= NM_000292.3:c.2404A>G
PHKA2 transcript NM_000292.2:c.2404= NM_000292.2:c.2404A>G
PHKA2 transcript variant X2 XM_005274548.6:c.2404= XM_005274548.6:c.2404A>G
PHKA2 transcript variant X2 XM_005274548.5:c.2404= XM_005274548.5:c.2404A>G
PHKA2 transcript variant X2 XM_005274548.4:c.2404= XM_005274548.4:c.2404A>G
PHKA2 transcript variant X2 XM_005274548.3:c.2404= XM_005274548.3:c.2404A>G
PHKA2 transcript variant X1 XM_005274548.2:c.2404= XM_005274548.2:c.2404A>G
PHKA2 transcript variant X1 XM_005274548.1:c.2404= XM_005274548.1:c.2404A>G
PHKA2 transcript variant X4 XM_005274550.6:c.2404= XM_005274550.6:c.2404A>G
PHKA2 transcript variant X4 XM_005274550.5:c.2404= XM_005274550.5:c.2404A>G
PHKA2 transcript variant X4 XM_005274550.4:c.2404= XM_005274550.4:c.2404A>G
PHKA2 transcript variant X4 XM_005274550.3:c.2404= XM_005274550.3:c.2404A>G
PHKA2 transcript variant X3 XM_005274550.2:c.2404= XM_005274550.2:c.2404A>G
PHKA2 transcript variant X3 XM_005274550.1:c.2404= XM_005274550.1:c.2404A>G
PHKA2 transcript variant X1 XM_006724496.5:c.2404= XM_006724496.5:c.2404A>G
PHKA2 transcript variant X1 XM_006724496.4:c.2404= XM_006724496.4:c.2404A>G
PHKA2 transcript variant X1 XM_006724496.3:c.2404= XM_006724496.3:c.2404A>G
PHKA2 transcript variant X1 XM_006724496.2:c.2404= XM_006724496.2:c.2404A>G
PHKA2 transcript variant X4 XM_006724496.1:c.2404= XM_006724496.1:c.2404A>G
PHKA2 transcript variant X3 XM_011545537.4:c.2305= XM_011545537.4:c.2305A>G
PHKA2 transcript variant X3 XM_011545537.3:c.2305= XM_011545537.3:c.2305A>G
PHKA2 transcript variant X3 XM_011545537.2:c.2305= XM_011545537.2:c.2305A>G
PHKA2 transcript variant X3 XM_011545537.1:c.2305= XM_011545537.1:c.2305A>G
PHKA2 transcript variant X8 XR_950461.4:n.2586= XR_950461.4:n.2586A>G
PHKA2 transcript variant X5 XR_950461.3:n.2574= XR_950461.3:n.2574A>G
PHKA2 transcript variant X5 XR_950461.2:n.2588= XR_950461.2:n.2588A>G
PHKA2 transcript variant X5 XR_950461.1:n.2588= XR_950461.1:n.2588A>G
PHKA2 transcript variant X12 XM_011545538.4:c.1387= XM_011545538.4:c.1387A>G
PHKA2 transcript variant X11 XM_011545538.3:c.1387= XM_011545538.3:c.1387A>G
PHKA2 transcript variant X10 XM_011545538.2:c.1387= XM_011545538.2:c.1387A>G
PHKA2 transcript variant X7 XM_011545538.1:c.1387= XM_011545538.1:c.1387A>G
PHKA2 transcript variant X11 XM_017029580.3:c.1498= XM_017029580.3:c.1498A>G
PHKA2 transcript variant X10 XM_017029580.2:c.1498= XM_017029580.2:c.1498A>G
PHKA2 transcript variant X9 XM_017029580.1:c.1498= XM_017029580.1:c.1498A>G
PHKA2 transcript variant X9 XR_001755697.3:n.2586= XR_001755697.3:n.2586A>G
PHKA2 transcript variant X6 XR_001755697.2:n.2574= XR_001755697.2:n.2574A>G
PHKA2 transcript variant X6 XR_001755697.1:n.2588= XR_001755697.1:n.2588A>G
PHKA2 transcript variant X5 XM_047442163.1:c.2305= XM_047442163.1:c.2305A>G
PHKA2 transcript variant X6 XM_047442164.1:c.2305= XM_047442164.1:c.2305A>G
PHKA2 transcript variant X7 XM_047442165.1:c.2305= XM_047442165.1:c.2305A>G
PHKA2 transcript variant X10 XM_047442166.1:c.1858= XM_047442166.1:c.1858A>G
phosphorylase b kinase regulatory subunit alpha, liver isoform NP_000283.1:p.Thr802= NP_000283.1:p.Thr802Ala
phosphorylase b kinase regulatory subunit alpha, liver isoform isoform X2 XP_005274605.1:p.Thr802= XP_005274605.1:p.Thr802Ala
phosphorylase b kinase regulatory subunit alpha, liver isoform isoform X4 XP_005274607.1:p.Thr802= XP_005274607.1:p.Thr802Ala
phosphorylase b kinase regulatory subunit alpha, liver isoform isoform X1 XP_006724559.1:p.Thr802= XP_006724559.1:p.Thr802Ala
phosphorylase b kinase regulatory subunit alpha, liver isoform isoform X3 XP_011543839.1:p.Thr769= XP_011543839.1:p.Thr769Ala
phosphorylase b kinase regulatory subunit alpha, liver isoform isoform X10 XP_011543840.1:p.Thr463= XP_011543840.1:p.Thr463Ala
phosphorylase b kinase regulatory subunit alpha, liver isoform isoform X9 XP_016885069.1:p.Thr500= XP_016885069.1:p.Thr500Ala
phosphorylase b kinase regulatory subunit alpha, liver isoform isoform X5 XP_047298119.1:p.Thr769= XP_047298119.1:p.Thr769Ala
phosphorylase b kinase regulatory subunit alpha, liver isoform isoform X6 XP_047298120.1:p.Thr769= XP_047298120.1:p.Thr769Ala
phosphorylase b kinase regulatory subunit alpha, liver isoform isoform X7 XP_047298121.1:p.Thr769= XP_047298121.1:p.Thr769Ala
phosphorylase b kinase regulatory subunit alpha, liver isoform isoform X8 XP_047298122.1:p.Thr620= XP_047298122.1:p.Thr620Ala
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#.

22 SubSNP, 5 Frequency submissions
No Submitter Submission ID Date (Build)
1 EXOME_CHIP ss491575386 May 04, 2012 (137)
2 EVA_EXAC ss1694469812 Apr 01, 2015 (144)
3 ILLUMINA ss1752802327 Sep 08, 2015 (146)
4 ILLUMINA ss1917716323 Feb 12, 2016 (147)
5 ILLUMINA ss1945969583 Feb 12, 2016 (147)
6 ILLUMINA ss1958179052 Feb 12, 2016 (147)
7 GNOMAD ss2745325253 Nov 08, 2017 (151)
8 AFFY ss2985481561 Nov 08, 2017 (151)
9 ILLUMINA ss3022993317 Nov 08, 2017 (151)
10 ILLUMINA ss3635243559 Oct 12, 2018 (152)
11 ILLUMINA ss3640951041 Oct 12, 2018 (152)
12 ILLUMINA ss3645009177 Oct 12, 2018 (152)
13 ILLUMINA ss3653551716 Oct 12, 2018 (152)
14 ILLUMINA ss3654247912 Oct 12, 2018 (152)
15 ILLUMINA ss3726665991 Jul 13, 2019 (153)
16 ILLUMINA ss3744597659 Jul 13, 2019 (153)
17 ILLUMINA ss3745543984 Jul 13, 2019 (153)
18 ILLUMINA ss3773035690 Jul 13, 2019 (153)
19 GNOMAD ss4368627119 Apr 27, 2021 (155)
20 TOPMED ss5116929170 Apr 27, 2021 (155)
21 EVA ss5848228748 Oct 16, 2022 (156)
22 EVA ss5977909788 Oct 16, 2022 (156)
23 ExAC NC_000023.10 - 18926131 Oct 12, 2018 (152)
24 gnomAD - Genomes NC_000023.11 - 18908013 Apr 27, 2021 (155)
25 gnomAD - Exomes NC_000023.10 - 18926131 Jul 13, 2019 (153)
26 TopMed NC_000023.11 - 18908013 Apr 27, 2021 (155)
27 ALFA NC_000023.11 - 18908013 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
9967830, 14661565, ss491575386, ss1694469812, ss1752802327, ss1917716323, ss1945969583, ss1958179052, ss2745325253, ss2985481561, ss3022993317, ss3635243559, ss3640951041, ss3645009177, ss3653551716, ss3654247912, ss3744597659, ss3745543984, ss3773035690, ss5848228748, ss5977909788 NC_000023.10:18926130:T:C NC_000023.11:18908012:T:C (self)
576281212, 680535527, 8659031893, ss3726665991, ss4368627119, ss5116929170 NC_000023.11:18908012:T:C NC_000023.11:18908012:T: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 rs144581707

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