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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.

rs199555648

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chrX:35802204 (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>G
Variation Type
SNV Single Nucleotide Variation
Frequency
G=0.001005 (266/264690, TOPMED)
G=0.000238 (43/180601, GnomAD_exome)
G=0.000148 (25/168546, ALFA) (+ 6 more)
G=0.000976 (101/103486, GnomAD)
G=0.00024 (20/83945, ExAC)
G=0.00029 (3/10302, GO-ESP)
G=0.0002 (1/4805, 1000G_30x)
G=0.0003 (1/3775, 1000G)
G=0.009 (1/108, Qatari)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
MAGEB16 : 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 168546 A=0.999852 G=0.000148
European Sub 146850 A=0.999973 G=0.000027
African Sub 4292 A=0.9953 G=0.0047
African Others Sub 168 A=1.000 G=0.000
African American Sub 4124 A=0.9952 G=0.0048
Asian Sub 6294 A=1.0000 G=0.0000
East Asian Sub 4476 A=1.0000 G=0.0000
Other Asian Sub 1818 A=1.0000 G=0.0000
Latin American 1 Sub 442 A=0.998 G=0.002
Latin American 2 Sub 950 A=1.000 G=0.000
South Asian Sub 280 A=1.000 G=0.000
Other Sub 9438 A=1.0000 G=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 A=0.998995 G=0.001005
gnomAD - Exomes Global Study-wide 180601 A=0.999762 G=0.000238
gnomAD - Exomes European Sub 96661 A=0.99999 G=0.00001
gnomAD - Exomes Asian Sub 32516 A=0.99997 G=0.00003
gnomAD - Exomes American Sub 27310 A=0.99974 G=0.00026
gnomAD - Exomes African Sub 12270 A=0.99739 G=0.00261
gnomAD - Exomes Ashkenazi Jewish Sub 7415 A=1.0000 G=0.0000
gnomAD - Exomes Other Sub 4429 A=0.9995 G=0.0005
Allele Frequency Aggregator Total Global 168546 A=0.999852 G=0.000148
Allele Frequency Aggregator European Sub 146850 A=0.999973 G=0.000027
Allele Frequency Aggregator Other Sub 9438 A=1.0000 G=0.0000
Allele Frequency Aggregator Asian Sub 6294 A=1.0000 G=0.0000
Allele Frequency Aggregator African Sub 4292 A=0.9953 G=0.0047
Allele Frequency Aggregator Latin American 2 Sub 950 A=1.000 G=0.000
Allele Frequency Aggregator Latin American 1 Sub 442 A=0.998 G=0.002
Allele Frequency Aggregator South Asian Sub 280 A=1.000 G=0.000
gnomAD - Genomes Global Study-wide 103486 A=0.999024 G=0.000976
gnomAD - Genomes European Sub 56933 A=1.00000 G=0.00000
gnomAD - Genomes African Sub 30997 A=0.99700 G=0.00300
gnomAD - Genomes American Sub 9252 A=0.9995 G=0.0005
gnomAD - Genomes Ashkenazi Jewish Sub 2516 A=1.0000 G=0.0000
gnomAD - Genomes East Asian Sub 2228 A=1.0000 G=0.0000
gnomAD - Genomes Other Sub 1560 A=0.9981 G=0.0019
ExAC Global Study-wide 83945 A=0.99976 G=0.00024
ExAC Europe Sub 50828 A=1.00000 G=0.00000
ExAC Asian Sub 15940 A=1.00000 G=0.00000
ExAC American Sub 9253 A=0.9997 G=0.0003
ExAC African Sub 7324 A=0.9977 G=0.0023
ExAC Other Sub 600 A=1.000 G=0.000
GO Exome Sequencing Project Global Study-wide 10302 A=0.99971 G=0.00029
GO Exome Sequencing Project European American Sub 6621 A=1.0000 G=0.0000
GO Exome Sequencing Project African American Sub 3681 A=0.9992 G=0.0008
1000Genomes_30x Global Study-wide 4805 A=0.9998 G=0.0002
1000Genomes_30x African Sub 1328 A=0.9992 G=0.0008
1000Genomes_30x Europe Sub 961 A=1.000 G=0.000
1000Genomes_30x South Asian Sub 883 A=1.000 G=0.000
1000Genomes_30x East Asian Sub 878 A=1.000 G=0.000
1000Genomes_30x American Sub 755 A=1.000 G=0.000
1000Genomes Global Study-wide 3775 A=0.9997 G=0.0003
1000Genomes African Sub 1003 A=0.9990 G=0.0010
1000Genomes Europe Sub 766 A=1.000 G=0.000
1000Genomes East Asian Sub 764 A=1.000 G=0.000
1000Genomes South Asian Sub 718 A=1.000 G=0.000
1000Genomes American Sub 524 A=1.000 G=0.000
Qatari Global Study-wide 108 A=0.991 G=0.009
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.35802204A>G
GRCh37.p13 chr X NC_000023.10:g.35820321A>G
Gene: MAGEB16, MAGE family member B16 (plus strand)
Molecule type Change Amino acid[Codon] SO Term
MAGEB16 transcript variant 2 NM_001099921.2:c.8A>G Q [CAG] > R [CGG] Coding Sequence Variant
melanoma-associated antigen B16 isoform 1 NP_001093391.1:p.Gln3Arg Q (Gln) > R (Arg) Missense Variant
MAGEB16 transcript variant 3 NM_001370159.1:c.8A>G Q [CAG] > R [CGG] Coding Sequence Variant
melanoma-associated antigen B16 isoform 1 NP_001357088.1:p.Gln3Arg Q (Gln) > R (Arg) Missense Variant
MAGEB16 transcript variant 1 NM_001370158.1:c.8A>G Q [CAG] > R [CGG] Coding Sequence Variant
melanoma-associated antigen B16 isoform 1 NP_001357087.1:p.Gln3Arg Q (Gln) > R (Arg) Missense 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 A= G
GRCh38.p14 chr X NC_000023.11:g.35802204= NC_000023.11:g.35802204A>G
GRCh37.p13 chr X NC_000023.10:g.35820321= NC_000023.10:g.35820321A>G
MAGEB16 transcript variant 2 NM_001099921.2:c.8= NM_001099921.2:c.8A>G
MAGEB16 transcript NM_001099921.1:c.8= NM_001099921.1:c.8A>G
MAGEB16 transcript variant 3 NM_001370159.1:c.8= NM_001370159.1:c.8A>G
MAGEB16 transcript variant 1 NM_001370158.1:c.8= NM_001370158.1:c.8A>G
melanoma-associated antigen B16 isoform 1 NP_001093391.1:p.Gln3= NP_001093391.1:p.Gln3Arg
melanoma-associated antigen B16 isoform 1 NP_001357088.1:p.Gln3= NP_001357088.1:p.Gln3Arg
melanoma-associated antigen B16 isoform 1 NP_001357087.1:p.Gln3= NP_001357087.1:p.Gln3Arg
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#.

34 SubSNP, 9 Frequency submissions
No Submitter Submission ID Date (Build)
1 EXOME_CHIP ss491575923 May 04, 2012 (137)
2 NHLBI-ESP ss713647431 Apr 25, 2013 (138)
3 ILLUMINA ss780765525 Sep 08, 2015 (146)
4 ILLUMINA ss783444833 Sep 08, 2015 (146)
5 1000GENOMES ss1554082273 Apr 01, 2015 (144)
6 EVA_EXAC ss1694488168 Apr 01, 2015 (144)
7 ILLUMINA ss1752805728 Sep 08, 2015 (146)
8 ILLUMINA ss1917716793 Feb 12, 2016 (147)
9 WEILL_CORNELL_DGM ss1939271071 Feb 12, 2016 (147)
10 ILLUMINA ss1945971620 Feb 12, 2016 (147)
11 ILLUMINA ss1958187696 Feb 12, 2016 (147)
12 HUMAN_LONGEVITY ss2316742672 Dec 20, 2016 (150)
13 GNOMAD ss2745352925 Nov 08, 2017 (151)
14 GNOMAD ss2746090510 Nov 08, 2017 (151)
15 GNOMAD ss2977915422 Nov 08, 2017 (151)
16 AFFY ss2985483269 Nov 08, 2017 (151)
17 ILLUMINA ss3023001333 Nov 08, 2017 (151)
18 ILLUMINA ss3630419882 Oct 12, 2018 (152)
19 ILLUMINA ss3635246631 Oct 12, 2018 (152)
20 ILLUMINA ss3640954113 Oct 12, 2018 (152)
21 ILLUMINA ss3645010664 Oct 12, 2018 (152)
22 ILLUMINA ss3653559813 Oct 12, 2018 (152)
23 ILLUMINA ss3654249770 Oct 12, 2018 (152)
24 ILLUMINA ss3726672834 Jul 13, 2019 (153)
25 ILLUMINA ss3744598143 Jul 13, 2019 (153)
26 ILLUMINA ss3745547049 Jul 13, 2019 (153)
27 ILLUMINA ss3773038756 Jul 13, 2019 (153)
28 EVA ss3825479321 Apr 27, 2020 (154)
29 TOPMED ss5120005123 Apr 26, 2021 (155)
30 HUGCELL_USP ss5503961668 Oct 16, 2022 (156)
31 1000G_HIGH_COVERAGE ss5620342680 Oct 16, 2022 (156)
32 SANFORD_IMAGENETICS ss5665097019 Oct 16, 2022 (156)
33 EVA ss5848230918 Oct 16, 2022 (156)
34 EVA ss5978086333 Oct 16, 2022 (156)
35 1000Genomes NC_000023.10 - 35820321 Oct 12, 2018 (152)
36 1000Genomes_30x NC_000023.11 - 35802204 Oct 16, 2022 (156)
37 ExAC NC_000023.10 - 35820321 Oct 12, 2018 (152)
38 gnomAD - Genomes NC_000023.11 - 35802204 Apr 26, 2021 (155)
39 gnomAD - Exomes NC_000023.10 - 35820321 Jul 13, 2019 (153)
40 GO Exome Sequencing Project NC_000023.10 - 35820321 Oct 12, 2018 (152)
41 Qatari NC_000023.10 - 35820321 Apr 27, 2020 (154)
42 TopMed NC_000023.11 - 35802204 Apr 26, 2021 (155)
43 ALFA NC_000023.11 - 35802204 Apr 26, 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
82060550, 9987650, 14689299, 1936116, 21312993, ss491575923, ss713647431, ss780765525, ss783444833, ss1554082273, ss1694488168, ss1752805728, ss1917716793, ss1939271071, ss1945971620, ss1958187696, ss2745352925, ss2746090510, ss2977915422, ss2985483269, ss3023001333, ss3630419882, ss3635246631, ss3640954113, ss3645010664, ss3653559813, ss3654249770, ss3744598143, ss3745547049, ss3773038756, ss3825479321, ss5665097019, ss5848230918, ss5978086333 NC_000023.10:35820320:A:G NC_000023.11:35802203:A:G (self)
107868615, 578577800, 683611480, 6374066812, ss2316742672, ss3726672834, ss5120005123, ss5503961668, ss5620342680 NC_000023.11:35802203:A:G NC_000023.11:35802203:A:G (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 rs199555648

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