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dbSNP Short Genetic Variations

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.

rs121912763

Current Build 152

Released October 2, 2018

Organism
Homo sapiens
Position
chr1:25303329 (GRCh38.p12) 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>G
Variation Type
SNV Single Nucleotide Variation
Frequency
G=0.00248 (539/217608, GnomAD)
G=0.0029 (270/92770, ExAC)
G=0.0025 (67/26324, GnomAD) (+ 1 more)
G=0.001 (6/5008, 1000G)
Clinical Significance
Reported in ClinVar
Gene : Consequence
RHD : Missense Variant
RSRP1 : Non Coding Transcript Variant
Publications
1 citation
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.p12 chr 1 NC_000001.11:g.25303329T>G
GRCh37.p13 chr 1 NC_000001.10:g.25629820T>G
RHD RefSeqGene NG_007494.1:g.35840T>G
Gene: RSRP1, arginine and serine rich protein 1 (minus strand)
Molecule type Change Amino acid[Codon] SO Term
RSRP1 transcript variant 14 NM_001321772.1:c. N/A Intron Variant
RSRP1 transcript variant 2 NM_020317.4:c. N/A Genic Upstream Transcript Variant
RSRP1 transcript variant 18 NR_135790.1:n.2917A>C N/A Non Coding Transcript Variant
RSRP1 transcript variant 20 NR_135792.1:n.2708A>C N/A Non Coding Transcript Variant
RSRP1 transcript variant 19 NR_135791.1:n.3096A>C N/A Non Coding Transcript Variant
RSRP1 transcript variant 21 NR_135793.1:n.2762A>C N/A Non Coding Transcript Variant
RSRP1 transcript variant 15 NR_135787.1:n. N/A Intron Variant
RSRP1 transcript variant 16 NR_135788.1:n. N/A Intron Variant
RSRP1 transcript variant 17 NR_135789.1:n. N/A Intron Variant
RSRP1 transcript variant 3 NR_135143.1:n. N/A Genic Upstream Transcript Variant
RSRP1 transcript variant 4 NR_135144.1:n. N/A Genic Upstream Transcript Variant
RSRP1 transcript variant 5 NR_135777.1:n. N/A Genic Upstream Transcript Variant
RSRP1 transcript variant 6 NR_135778.1:n. N/A Genic Upstream Transcript Variant
RSRP1 transcript variant 7 NR_135780.1:n. N/A Genic Upstream Transcript Variant
RSRP1 transcript variant 8 NR_135781.1:n. N/A Genic Upstream Transcript Variant
RSRP1 transcript variant 9 NR_135782.1:n. N/A Genic Upstream Transcript Variant
RSRP1 transcript variant 10 NR_135783.1:n. N/A Genic Upstream Transcript Variant
RSRP1 transcript variant 11 NR_135784.1:n. N/A Genic Upstream Transcript Variant
RSRP1 transcript variant 12 NR_135785.1:n. N/A Genic Upstream Transcript Variant
RSRP1 transcript variant 13 NR_135786.1:n. N/A Genic Upstream 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 1 NM_016124.4:c.809T>G V [GTG] > G [GGG] Coding Sequence Variant
blood group Rh(D) polypeptide isoform 1 NP_057208.2:p.Val270Gly V (Val) > G (Gly) Missense Variant
RHD transcript variant 2 NM_001127691.2:c.809T>G V [GTG] > G [GGG] Coding Sequence Variant
blood group Rh(D) polypeptide isoform 2 NP_001121163.1:p.Val270Gly V (Val) > G (Gly) Missense Variant
RHD transcript variant 3 NM_001282867.1:c.311T>G V [GTG] > G [GGG] Coding Sequence Variant
blood group Rh(D) polypeptide isoform 3 NP_001269796.1:p.Val104Gly V (Val) > G (Gly) Missense Variant
RHD transcript variant 4 NM_001282868.1:c.809T>G V [GTG] > G [GGG] Coding Sequence Variant
blood group Rh(D) polypeptide isoform 4 NP_001269797.1:p.Val270Gly V (Val) > G (Gly) Missense Variant
RHD transcript variant 5 NM_001282869.1:c.809T>G V [GTG] > G [GGG] Coding Sequence Variant
blood group Rh(D) polypeptide isoform 5 NP_001269798.1:p.Val270Gly V (Val) > G (Gly) Missense Variant
RHD transcript variant 6 NM_001282870.1:c.809T>G V [GTG] > G [GGG] Coding Sequence Variant
blood group Rh(D) polypeptide isoform 6 NP_001269799.1:p.Val270Gly V (Val) > G (Gly) Missense Variant
RHD transcript variant 7 NM_001282871.1:c.809T>G V [GTG] > G [GGG] Coding Sequence Variant
blood group Rh(D) polypeptide isoform 7 NP_001269800.1:p.Val270Gly V (Val) > G (Gly) Missense Variant
RHD transcript variant 8 NM_001282872.1:c.809T>G V [GTG] > G [GGG] Coding Sequence Variant
blood group Rh(D) polypeptide isoform 8 NP_001269801.1:p.Val270Gly V (Val) > G (Gly) Missense Variant
RHD transcript variant X1 XM_017002015.1:c.809T>G V [GTG] > G [GGG] Coding Sequence Variant
blood group Rh(D) polypeptide isoform X1 XP_016857504.1:p.Val270Gly V (Val) > G (Gly) Missense Variant
RHD transcript variant X2 XR_946736.1:n.964T>G N/A Non Coding Transcript Variant
RHD transcript variant X3 XR_946737.2:n.964T>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.

Allele: G (allele ID: 32752 )
ClinVar Accession Disease Names Clinical Significance
RCV000019287.27 Rhd, weak d, type I Pathogenic
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 217608 T=0.99752 G=0.00248
gnomAD - Exomes European Sub 111492 T=0.99610 G=0.00390
gnomAD - Exomes Asian Sub 45900 T=1.0000 G=0.0000
gnomAD - Exomes American Sub 31984 T=0.9987 G=0.0013
gnomAD - Exomes African Sub 14478 T=0.9990 G=0.0010
gnomAD - Exomes Ashkenazi Jewish Sub 8926 T=0.995 G=0.005
gnomAD - Exomes Other Sub 4828 T=0.999 G=0.001
ExAC Global Study-wide 92770 T=0.9971 G=0.0029
ExAC Europe Sub 51136 T=0.9951 G=0.0049
ExAC Asian Sub 22546 T=1.0000 G=0.0000
ExAC American Sub 9510 T=0.999 G=0.001
ExAC African Sub 8868 T=0.999 G=0.001
ExAC Other Sub 710 T=1.00 G=0.00
gnomAD - Genomes Global Study-wide 26324 T=0.9975 G=0.0025
gnomAD - Genomes European Sub 14830 T=0.9962 G=0.0038
gnomAD - Genomes African Sub 8034 T=0.999 G=0.001
gnomAD - Genomes East Asian Sub 1596 T=1.000 G=0.000
gnomAD - Genomes American Sub 798 T=1.00 G=0.00
gnomAD - Genomes Other Sub 788 T=1.00 G=0.00
gnomAD - Genomes Ashkenazi Jewish Sub 278 T=1.00 G=0.00
1000Genomes Global Study-wide 5008 T=0.999 G=0.001
1000Genomes African Sub 1322 T=0.998 G=0.002
1000Genomes East Asian Sub 1008 T=1.000 G=0.000
1000Genomes Europe Sub 1006 T=0.996 G=0.004
1000Genomes South Asian Sub 978 T=1.00 G=0.00
1000Genomes American Sub 694 T=1.00 G=0.00
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= G Note
GRCh38.p12 chr 1 NC_000001.11:g.25303329T= NC_000001.11:g.25303329T>G
GRCh37.p13 chr 1 NC_000001.10:g.25629820T= NC_000001.10:g.25629820T>G
RHD RefSeqGene NG_007494.1:g.35840T= NG_007494.1:g.35840T>G
RHD transcript variant 1 NM_016124.4:c.809T= NM_016124.4:c.809T>G
RHD transcript variant 1 NM_016124.3:c.809T= NM_016124.3:c.809T>G
RHD transcript variant 2 NM_001127691.2:c.809T= NM_001127691.2:c.809T>G
RHD transcript variant 2 NM_001127691.1:c.809T= NM_001127691.1:c.809T>G
RHD transcript variant 8 NM_001282872.1:c.809T= NM_001282872.1:c.809T>G
RHD transcript variant 7 NM_001282871.1:c.809T= NM_001282871.1:c.809T>G
RHD transcript variant 3 NM_001282867.1:c.311T= NM_001282867.1:c.311T>G
RHD transcript variant 6 NM_001282870.1:c.809T= NM_001282870.1:c.809T>G
RHD transcript variant 5 NM_001282869.1:c.809T= NM_001282869.1:c.809T>G
RHD transcript variant 4 NM_001282868.1:c.809T= NM_001282868.1:c.809T>G
RHD transcript variant X3 XR_946737.2:n.964T= XR_946737.2:n.964T>G
RSRP1 transcript variant 19 NR_135791.1:n.3096A= NR_135791.1:n.3096A>C
RSRP1 transcript variant 18 NR_135790.1:n.2917A= NR_135790.1:n.2917A>C
RSRP1 transcript variant 21 NR_135793.1:n.2762A= NR_135793.1:n.2762A>C
RSRP1 transcript variant 20 NR_135792.1:n.2708A= NR_135792.1:n.2708A>C
RHD transcript variant X1 XM_017002015.1:c.809T= XM_017002015.1:c.809T>G
RHD transcript variant X2 XR_946736.1:n.964T= XR_946736.1:n.964T>G
blood group Rh(D) polypeptide isoform 1 NP_057208.2:p.Val270= NP_057208.2:p.Val270Gly
blood group Rh(D) polypeptide isoform 2 NP_001121163.1:p.Val270= NP_001121163.1:p.Val270Gly
blood group Rh(D) polypeptide isoform 8 NP_001269801.1:p.Val270= NP_001269801.1:p.Val270Gly
blood group Rh(D) polypeptide isoform 7 NP_001269800.1:p.Val270= NP_001269800.1:p.Val270Gly
blood group Rh(D) polypeptide isoform 3 NP_001269796.1:p.Val104= NP_001269796.1:p.Val104Gly
blood group Rh(D) polypeptide isoform 6 NP_001269799.1:p.Val270= NP_001269799.1:p.Val270Gly
blood group Rh(D) polypeptide isoform 5 NP_001269798.1:p.Val270= NP_001269798.1:p.Val270Gly
blood group Rh(D) polypeptide isoform 4 NP_001269797.1:p.Val270= NP_001269797.1:p.Val270Gly
blood group Rh(D) polypeptide isoform X1 XP_016857504.1:p.Val270= XP_016857504.1:p.Val270Gly
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#.

11 SubSNP, 4 Frequency, 1 ClinVar submissions
No Submitter Submission ID Date (Build)
1 OMIM-CURATED-RECORDS ss275514004 Nov 22, 2010 (133)
2 NHLBI-ESP ss341945931 May 09, 2011 (134)
3 1000GENOMES ss488657973 May 04, 2012 (137)
4 EXOME_CHIP ss491289445 May 04, 2012 (137)
5 1000GENOMES ss1290089474 Aug 21, 2014 (142)
6 EVA_EXAC ss1685398867 Apr 01, 2015 (144)
7 GNOMAD ss2731264890 Nov 08, 2017 (151)
8 GNOMAD ss2746262148 Nov 08, 2017 (151)
9 GNOMAD ss2752823142 Nov 08, 2017 (151)
10 SWEGEN ss2986488886 Nov 08, 2017 (151)
11 TOPMED ss3071294443 Nov 08, 2017 (151)
12 1000Genomes NC_000001.10 - 25629820 Oct 11, 2018 (152)
13 ExAC NC_000001.10 - 25629820 Oct 11, 2018 (152)
14 gnomAD - Genomes NC_000001.10 - 25629820 Oct 11, 2018 (152)
15 gnomAD - Exomes NC_000001.10 - 25629820 Oct 11, 2018 (152)
16 ClinVar RCV000019287.27 Oct 11, 2018 (152)
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
779449, 4584578, 2222341, 209602, ss341945931, ss488657973, ss491289445, ss1290089474, ss1685398867, ss2731264890, ss2746262148, ss2752823142, ss2986488886 NC_000001.10:25629819:T= NC_000001.11:25303328:T= (self)
ss275514004, ss3071294443 NC_000001.11:25303328:T= NC_000001.11:25303328:T= (self)
779449, 4584578, 2222341, 209602, ss341945931, ss488657973, ss491289445, ss1290089474, ss1685398867, ss2731264890, ss2746262148, ss2752823142, ss2986488886 NC_000001.10:25629819:T>G NC_000001.11:25303328:T>G (self)
RCV000019287.27, ss275514004, ss3071294443 NC_000001.11:25303328:T>G NC_000001.11:25303328:T>G (self)
Help

Publications tab displays PubMed articles citing the variation as a listing of PMID, Title, Author, Year, Journal, ordered by Year, descending.

1 citation for rs121912763
PMID Title Author Year Journal
9864185 Molecular basis of weak D phenotypes. Wagner FF et al. 1999 Blood

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.post104+4a6ee9c