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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.

rs199509194

Current Build 155

Released April 9, 2021

Organism
Homo sapiens
Position
chr1:25284610 (GRCh38.p13) 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
G>T
Variation Type
SNV Single Nucleotide Variation
Frequency
T=0.005586 (1259/225376, GnomAD_exome)
T=0.022156 (2740/123668, GnomAD)
T=0.006653 (710/106724, ExAC) (+ 7 more)
T=0.00991 (194/19582, ALFA)
T=0.02480 (290/11692, GO-ESP)
T=0.1422 (712/5008, 1000G)
T=0.002 (1/534, MGP)
T=0.015 (3/202, Qatari)
G=0.50 (7/14, SGDP_PRJ)
T=0.50 (7/14, SGDP_PRJ)
Clinical Significance
Reported in ClinVar
Gene : Consequence
RHD : Missense Variant
RSRP1 : Intron Variant
Publications
0 citations
Genomic View
See rs on genome
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.p13 chr 1 NC_000001.11:g.25284610G>T
GRCh37.p13 chr 1 NC_000001.10:g.25611101G>T
RHD RefSeqGene (LRG_796) NG_007494.1:g.17121G>T
Gene: RSRP1, arginine and serine rich protein 1 (minus strand)
Molecule type Change Amino acid[Codon] SO Term
RSRP1 transcript variant 14 NM_001321772.2:c.-66-3758…

NM_001321772.2:c.-66-37581C>A

N/A Intron Variant
RSRP1 transcript variant 2 NM_020317.5:c. N/A Genic Upstream Transcript Variant
RSRP1 transcript variant 15 NR_135787.2:n. N/A Intron Variant
RSRP1 transcript variant 16 NR_135788.2:n. N/A Intron Variant
RSRP1 transcript variant 17 NR_135789.2:n. N/A Intron Variant
RSRP1 transcript variant 3 NR_135143.2:n. N/A Genic Upstream Transcript Variant
RSRP1 transcript variant 4 NR_135144.2:n. N/A Genic Upstream Transcript Variant
RSRP1 transcript variant 5 NR_135777.2:n. N/A Genic Upstream Transcript Variant
RSRP1 transcript variant 6 NR_135778.2:n. N/A Genic Upstream Transcript Variant
RSRP1 transcript variant 7 NR_135780.2:n. N/A Genic Upstream Transcript Variant
RSRP1 transcript variant 8 NR_135781.2:n. N/A Genic Upstream Transcript Variant
RSRP1 transcript variant 9 NR_135782.2:n. N/A Genic Upstream Transcript Variant
RSRP1 transcript variant 10 NR_135783.2:n. N/A Genic Upstream Transcript Variant
RSRP1 transcript variant 11 NR_135784.2:n. N/A Genic Upstream Transcript Variant
RSRP1 transcript variant 12 NR_135785.2:n. N/A Genic Upstream Transcript Variant
RSRP1 transcript variant 13 NR_135786.2:n. N/A Genic Upstream Transcript Variant
RSRP1 transcript variant 18 NR_135790.1:n. N/A Genic Downstream Transcript Variant
RSRP1 transcript variant 19 NR_135791.1:n. N/A Genic Downstream Transcript Variant
RSRP1 transcript variant 20 NR_135792.1:n. N/A Genic Downstream Transcript Variant
RSRP1 transcript variant 21 NR_135793.1:n. N/A Genic Downstream Transcript Variant
RSRP1 transcript variant X1 XM_011541797.1:c. N/A Genic Upstream Transcript Variant
RSRP1 transcript variant X2 XR_946709.2:n. N/A Genic Upstream Transcript Variant
Gene: RHD, Rh blood group D antigen (plus strand)
Molecule type Change Amino acid[Codon] SO Term
RHD transcript variant 3 NM_001282867.1:c.-309= N/A 5 Prime UTR Variant
RHD transcript variant 4 NM_001282868.1:c.186G>T L [TTG] > F [TTT] Coding Sequence Variant
blood group Rh(D) polypeptide isoform 4 NP_001269797.1:p.Leu62Phe L (Leu) > F (Phe) Missense Variant
RHD transcript variant 6 NM_001282870.1:c.186G>T L [TTG] > F [TTT] Coding Sequence Variant
blood group Rh(D) polypeptide isoform 6 NP_001269799.1:p.Leu62Phe L (Leu) > F (Phe) Missense Variant
RHD transcript variant 8 NM_001282872.1:c.186G>T L [TTG] > F [TTT] Coding Sequence Variant
blood group Rh(D) polypeptide isoform 8 NP_001269801.1:p.Leu62Phe L (Leu) > F (Phe) Missense Variant
RHD transcript variant 2 NM_001127691.3:c.186G>T L [TTG] > F [TTT] Coding Sequence Variant
blood group Rh(D) polypeptide isoform 2 NP_001121163.1:p.Leu62Phe L (Leu) > F (Phe) Missense Variant
RHD transcript variant 5 NM_001282869.2:c.186G>T L [TTG] > F [TTT] Coding Sequence Variant
blood group Rh(D) polypeptide isoform 5 NP_001269798.1:p.Leu62Phe L (Leu) > F (Phe) Missense Variant
RHD transcript variant 7 NM_001282871.2:c.186G>T L [TTG] > F [TTT] Coding Sequence Variant
blood group Rh(D) polypeptide isoform 7 NP_001269800.1:p.Leu62Phe L (Leu) > F (Phe) Missense Variant
RHD transcript variant 1 NM_016124.5:c.186G>T L [TTG] > F [TTT] Coding Sequence Variant
blood group Rh(D) polypeptide isoform 1 NP_057208.2:p.Leu62Phe L (Leu) > F (Phe) Missense Variant
RHD transcript variant X1 XM_017002015.1:c.186G>T L [TTG] > F [TTT] Coding Sequence Variant
blood group Rh(D) polypeptide isoform X1 XP_016857504.1:p.Leu62Phe L (Leu) > F (Phe) Missense Variant
RHD transcript variant X2 XR_946736.1:n.341G>T N/A Non Coding Transcript Variant
RHD transcript variant X3 XR_946737.2:n.341G>T 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.

Allele: T (allele ID: 622837 )
ClinVar Accession Disease Names Clinical Significance
RCV000785870.1 Partial RhD Not-Provided

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: 20201027095038
Population Group Sample Size Ref Allele Alt Allele
Total Global 19582 G=0.99009 T=0.00991
European Sub 13974 G=0.99950 T=0.00050
African Sub 3318 G=0.9494 T=0.0506
African Others Sub 108 G=0.944 T=0.056
African American Sub 3210 G=0.9495 T=0.0505
Asian Sub 146 G=1.000 T=0.000
East Asian Sub 120 G=1.000 T=0.000
Other Asian Sub 26 G=1.00 T=0.00
Latin American 1 Sub 154 G=0.994 T=0.006
Latin American 2 Sub 616 G=0.990 T=0.010
South Asian Sub 100 G=1.00 T=0.00
Other Sub 1274 G=0.9906 T=0.0094


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
gnomAD - Exomes Global Study-wide 225376 G=0.994414 T=0.005586
gnomAD - Exomes European Sub 114982 G=0.999800 T=0.000200
gnomAD - Exomes Asian Sub 47132 G=0.99987 T=0.00013
gnomAD - Exomes American Sub 33100 G=0.99662 T=0.00338
gnomAD - Exomes African Sub 15482 G=0.93224 T=0.06776
gnomAD - Exomes Ashkenazi Jewish Sub 9206 G=0.9952 T=0.0048
gnomAD - Exomes Other Sub 5474 G=0.9954 T=0.0046
gnomAD - Genomes Global Study-wide 123668 G=0.977844 T=0.022156
gnomAD - Genomes European Sub 63854 G=0.99973 T=0.00027
gnomAD - Genomes African Sub 39316 G=0.93509 T=0.06491
gnomAD - Genomes American Sub 12454 G=0.99012 T=0.00988
gnomAD - Genomes East Asian Sub 3120 G=1.0000 T=0.0000
gnomAD - Genomes Ashkenazi Jewish Sub 3014 G=0.9950 T=0.0050
gnomAD - Genomes Other Sub 1910 G=0.9827 T=0.0173
ExAC Global Study-wide 106724 G=0.993347 T=0.006653
ExAC Europe Sub 61386 G=0.99961 T=0.00039
ExAC Asian Sub 23922 G=0.99975 T=0.00025
ExAC American Sub 11010 G=0.99800 T=0.00200
ExAC African Sub 9590 G=0.9317 T=0.0683
ExAC Other Sub 816 G=0.996 T=0.004
GO Exome Sequencing Project Global Study-wide 11692 G=0.97520 T=0.02480
GO Exome Sequencing Project European American Sub 7430 G=0.9993 T=0.0007
GO Exome Sequencing Project African American Sub 4262 G=0.9331 T=0.0669
1000Genomes Global Study-wide 5008 G=0.8578 T=0.1422
1000Genomes African Sub 1322 G=0.8585 T=0.1415
1000Genomes East Asian Sub 1008 G=0.7341 T=0.2659
1000Genomes Europe Sub 1006 G=0.8529 T=0.1471
1000Genomes South Asian Sub 978 G=0.972 T=0.028
1000Genomes American Sub 694 G=0.882 T=0.118
Medical Genome Project healthy controls from Spanish population Spanish controls Study-wide 534 G=0.998 T=0.002
Qatari Global Study-wide 202 G=0.985 T=0.015
SGDP_PRJ Global Study-wide 14 G=0.50 T=0.50
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 G= T
GRCh38.p13 chr 1 NC_000001.11:g.25284610= NC_000001.11:g.25284610G>T
GRCh37.p13 chr 1 NC_000001.10:g.25611101= NC_000001.10:g.25611101G>T
RHD RefSeqGene (LRG_796) NG_007494.1:g.17121= NG_007494.1:g.17121G>T
RHD transcript variant 1 NM_016124.4:c.186= NM_016124.4:c.186G>T
RHD transcript variant 1 NM_016124.5:c.186= NM_016124.5:c.186G>T
RHD transcript variant 1 NM_016124.3:c.186= NM_016124.3:c.186G>T
RHD transcript variant 2 NM_001127691.3:c.186= NM_001127691.3:c.186G>T
RHD transcript variant 2 NM_001127691.2:c.186= NM_001127691.2:c.186G>T
RHD transcript variant 2 NM_001127691.1:c.186= NM_001127691.1:c.186G>T
RHD transcript variant 7 NM_001282871.2:c.186= NM_001282871.2:c.186G>T
RHD transcript variant 7 NM_001282871.1:c.186= NM_001282871.1:c.186G>T
RHD transcript variant 5 NM_001282869.2:c.186= NM_001282869.2:c.186G>T
RHD transcript variant 5 NM_001282869.1:c.186= NM_001282869.1:c.186G>T
RHD transcript variant 8 NM_001282872.1:c.186= NM_001282872.1:c.186G>T
RHD transcript variant 3 NM_001282867.1:c.-309= NM_001282867.1:c.-309G>T
RHD transcript variant 6 NM_001282870.1:c.186= NM_001282870.1:c.186G>T
RHD transcript variant 4 NM_001282868.1:c.186= NM_001282868.1:c.186G>T
RHD transcript variant 2 NM_016225.3:c.186= NM_016225.3:c.186G>T
RHD transcript variant 2 NM_016225.2:c.186= NM_016225.2:c.186G>T
RHD transcript variant X3 XR_946737.2:n.341= XR_946737.2:n.341G>T
RHD transcript variant X1 XM_017002015.1:c.186= XM_017002015.1:c.186G>T
RHD transcript variant X2 XR_946736.1:n.341= XR_946736.1:n.341G>T
LOC51698 transcript NM_016225.1:c.186= NM_016225.1:c.186G>T
blood group Rh(D) polypeptide isoform 1 NP_057208.2:p.Leu62= NP_057208.2:p.Leu62Phe
blood group Rh(D) polypeptide isoform 2 NP_001121163.1:p.Leu62= NP_001121163.1:p.Leu62Phe
blood group Rh(D) polypeptide isoform 7 NP_001269800.1:p.Leu62= NP_001269800.1:p.Leu62Phe
blood group Rh(D) polypeptide isoform 5 NP_001269798.1:p.Leu62= NP_001269798.1:p.Leu62Phe
blood group Rh(D) polypeptide isoform 8 NP_001269801.1:p.Leu62= NP_001269801.1:p.Leu62Phe
blood group Rh(D) polypeptide isoform 6 NP_001269799.1:p.Leu62= NP_001269799.1:p.Leu62Phe
blood group Rh(D) polypeptide isoform 4 NP_001269797.1:p.Leu62= NP_001269797.1:p.Leu62Phe
blood group Rh(D) polypeptide isoform X1 XP_016857504.1:p.Leu62= XP_016857504.1:p.Leu62Phe
RSRP1 transcript variant 14 NM_001321772.2:c.-66-37581= NM_001321772.2:c.-66-37581C>A
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#.

26 SubSNP, 9 Frequency, 1 ClinVar submissions
No Submitter Submission ID Date (Build)
1 1000GENOMES ss488657942 May 04, 2012 (137)
2 EXOME_CHIP ss491289424 May 04, 2012 (137)
3 CLINSEQ_SNP ss491589276 May 04, 2012 (137)
4 ILLUMINA ss533997753 Sep 08, 2015 (146)
5 NHLBI-ESP ss712285170 Apr 25, 2013 (138)
6 1000GENOMES ss1290088918 Aug 21, 2014 (142)
7 DDI ss1425750371 Apr 01, 2015 (144)
8 EVA_EXAC ss1685398660 Apr 01, 2015 (144)
9 EVA_MGP ss1710896015 Apr 01, 2015 (144)
10 WEILL_CORNELL_DGM ss1918171984 Feb 12, 2016 (147)
11 ILLUMINA ss1958254299 Feb 12, 2016 (147)
12 GNOMAD ss2731264593 Nov 08, 2017 (151)
13 GNOMAD ss2746262052 Nov 08, 2017 (151)
14 GNOMAD ss2752821591 Nov 08, 2017 (151)
15 AFFY ss2984850835 Nov 08, 2017 (151)
16 ILLUMINA ss3021067955 Nov 08, 2017 (151)
17 TOPMED ss3071291161 Nov 08, 2017 (151)
18 ILLUMINA ss3626051758 Oct 11, 2018 (152)
19 ILLUMINA ss3651393375 Oct 11, 2018 (152)
20 ILLUMINA ss3653623903 Oct 11, 2018 (152)
21 ILLUMINA ss3725007216 Jul 12, 2019 (153)
22 EVA ss3745957030 Jul 12, 2019 (153)
23 KHV_HUMAN_GENOMES ss3798977283 Jul 12, 2019 (153)
24 EVA ss3823579768 Apr 25, 2020 (154)
25 SGDP_PRJ ss3848437948 Apr 25, 2020 (154)
26 EVA ss3986108070 Apr 25, 2021 (155)
27 1000Genomes NC_000001.10 - 25611101 Oct 11, 2018 (152)
28 ExAC NC_000001.10 - 25611101 Oct 11, 2018 (152)
29 gnomAD - Genomes NC_000001.11 - 25284610 Apr 25, 2021 (155)
30 gnomAD - Exomes NC_000001.10 - 25611101 Jul 12, 2019 (153)
31 GO Exome Sequencing Project NC_000001.10 - 25611101 Oct 11, 2018 (152)
32 Medical Genome Project healthy controls from Spanish population NC_000001.10 - 25611101 Apr 25, 2020 (154)
33 Qatari NC_000001.10 - 25611101 Apr 25, 2020 (154)
34 SGDP_PRJ NC_000001.10 - 25611101 Apr 25, 2020 (154)
35 ALFA NC_000001.11 - 25284610 Apr 25, 2021 (155)
36 ClinVar RCV000785870.1 Jul 12, 2019 (153)
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
ss491589276 NC_000001.9:25483687:G:T NC_000001.11:25284609:G:T (self)
778879, 4584354, 278526, 38472, 12767, 213914, 454928, ss488657942, ss491289424, ss533997753, ss712285170, ss1290088918, ss1425750371, ss1685398660, ss1710896015, ss1918171984, ss1958254299, ss2731264593, ss2746262052, ss2752821591, ss2984850835, ss3021067955, ss3626051758, ss3651393375, ss3653623903, ss3745957030, ss3823579768, ss3848437948, ss3986108070 NC_000001.10:25611100:G:T NC_000001.11:25284609:G:T (self)
RCV000785870.1, 5446063, 6359137726, ss3071291161, ss3725007216, ss3798977283 NC_000001.11:25284609:G:T NC_000001.11:25284609:G: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 rs199509194

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.post596+ae089ad