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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.

rs1053356

Current Build 155

Released April 9, 2021

Organism
Homo sapiens
Position
chr1:25301552 (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
T>G
Variation Type
SNV Single Nucleotide Variation
Frequency
G=0.010346 (2328/225016, GnomAD_exome)
G=0.036481 (4411/120912, GnomAD)
G=0.012114 (1312/108300, ExAC) (+ 12 more)
G=0.00054 (9/16672, 8.3KJPN)
G=0.02910 (356/12232, ALFA)
G=0.03398 (400/11770, GO-ESP)
G=0.0341 (171/5008, 1000G)
G=0.0023 (9/3854, ALSPAC)
G=0.0013 (5/3708, TWINSUK)
G=0.0007 (2/2914, KOREAN)
G=0.001 (1/998, GoNL)
G=0.007 (4/534, MGP)
G=0.018 (9/504, NorthernSweden)
G=0.025 (5/202, Qatari)
T=0.42 (10/24, SGDP_PRJ)
Clinical Significance
Reported in ClinVar
Gene : Consequence
RHD : Missense Variant
RSRP1 : Intron 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.p13 chr 1 NC_000001.11:g.25301552T>G
GRCh37.p13 chr 1 NC_000001.10:g.25628043T>G
RHD RefSeqGene (LRG_796) NG_007494.1:g.34063T>G
Gene: RSRP1, arginine and serine rich protein 1 (minus strand)
Molecule type Change Amino acid[Codon] SO Term
RSRP1 transcript variant 14 NM_001321772.2:c.-67+3548…

NM_001321772.2:c.-67+35488A>C

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.169T>G F [TTC] > V [GTC] Coding Sequence Variant
blood group Rh(D) polypeptide isoform 3 NP_001269796.1:p.Phe57Val F (Phe) > V (Val) Missense Variant
RHD transcript variant 4 NM_001282868.1:c.667T>G F [TTC] > V [GTC] Coding Sequence Variant
blood group Rh(D) polypeptide isoform 4 NP_001269797.1:p.Phe223Val F (Phe) > V (Val) Missense Variant
RHD transcript variant 6 NM_001282870.1:c.667T>G F [TTC] > V [GTC] Coding Sequence Variant
blood group Rh(D) polypeptide isoform 6 NP_001269799.1:p.Phe223Val F (Phe) > V (Val) Missense Variant
RHD transcript variant 8 NM_001282872.1:c.667T>G F [TTC] > V [GTC] Coding Sequence Variant
blood group Rh(D) polypeptide isoform 8 NP_001269801.1:p.Phe223Val F (Phe) > V (Val) Missense Variant
RHD transcript variant 2 NM_001127691.3:c.667T>G F [TTC] > V [GTC] Coding Sequence Variant
blood group Rh(D) polypeptide isoform 2 NP_001121163.1:p.Phe223Val F (Phe) > V (Val) Missense Variant
RHD transcript variant 5 NM_001282869.2:c.667T>G F [TTC] > V [GTC] Coding Sequence Variant
blood group Rh(D) polypeptide isoform 5 NP_001269798.1:p.Phe223Val F (Phe) > V (Val) Missense Variant
RHD transcript variant 7 NM_001282871.2:c.667T>G F [TTC] > V [GTC] Coding Sequence Variant
blood group Rh(D) polypeptide isoform 7 NP_001269800.1:p.Phe223Val F (Phe) > V (Val) Missense Variant
RHD transcript variant 1 NM_016124.5:c.667T>G F [TTC] > V [GTC] Coding Sequence Variant
blood group Rh(D) polypeptide isoform 1 NP_057208.2:p.Phe223Val F (Phe) > V (Val) Missense Variant
RHD transcript variant X1 XM_017002015.1:c.667T>G F [TTC] > V [GTC] Coding Sequence Variant
blood group Rh(D) polypeptide isoform X1 XP_016857504.1:p.Phe223Val F (Phe) > V (Val) Missense Variant
RHD transcript variant X2 XR_946736.1:n.822T>G N/A Non Coding Transcript Variant
RHD transcript variant X3 XR_946737.2:n.822T>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: 198597 )
ClinVar Accession Disease Names Clinical Significance
RCV000184007.1 Weak RhD expression Not-Provided
RCV000190496.1 Weak RhD expression Not-Provided
RCV000785870.1 Partial RhD Not-Provided
RCV000785871.1 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 12232 T=0.97090 G=0.02910
European Sub 7752 T=0.9985 G=0.0015
African Sub 2864 T=0.8925 G=0.1075
African Others Sub 108 T=0.889 G=0.111
African American Sub 2756 T=0.8926 G=0.1074
Asian Sub 108 T=1.000 G=0.000
East Asian Sub 84 T=1.00 G=0.00
Other Asian Sub 24 T=1.00 G=0.00
Latin American 1 Sub 146 T=0.966 G=0.034
Latin American 2 Sub 610 T=0.985 G=0.015
South Asian Sub 94 T=1.00 G=0.00
Other Sub 658 T=0.967 G=0.033


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 225016 T=0.989654 G=0.010346
gnomAD - Exomes European Sub 114832 T=0.998781 G=0.001219
gnomAD - Exomes Asian Sub 46996 T=0.99700 G=0.00300
gnomAD - Exomes American Sub 33048 T=0.99216 G=0.00784
gnomAD - Exomes African Sub 15482 T=0.88890 G=0.11110
gnomAD - Exomes Ashkenazi Jewish Sub 9188 T=0.9963 G=0.0037
gnomAD - Exomes Other Sub 5470 T=0.9938 G=0.0062
gnomAD - Genomes Global Study-wide 120912 T=0.963519 G=0.036481
gnomAD - Genomes European Sub 62318 T=0.99913 G=0.00087
gnomAD - Genomes African Sub 38440 T=0.89454 G=0.10546
gnomAD - Genomes American Sub 12168 T=0.98192 G=0.01808
gnomAD - Genomes East Asian Sub 3118 T=0.9968 G=0.0032
gnomAD - Genomes Ashkenazi Jewish Sub 3000 T=0.9953 G=0.0047
gnomAD - Genomes Other Sub 1868 T=0.9684 G=0.0316
ExAC Global Study-wide 108300 T=0.987886 G=0.012114
ExAC Europe Sub 62388 T=0.99848 G=0.00152
ExAC Asian Sub 23992 T=0.99692 G=0.00308
ExAC American Sub 11132 T=0.99470 G=0.00530
ExAC African Sub 9954 T=0.8914 G=0.1086
ExAC Other Sub 834 T=0.996 G=0.004
8.3KJPN JAPANESE Study-wide 16672 T=0.99946 G=0.00054
GO Exome Sequencing Project Global Study-wide 11770 T=0.96602 G=0.03398
GO Exome Sequencing Project European American Sub 7528 T=0.9979 G=0.0021
GO Exome Sequencing Project African American Sub 4242 T=0.9095 G=0.0905
1000Genomes Global Study-wide 5008 T=0.9659 G=0.0341
1000Genomes African Sub 1322 T=0.8820 G=0.1180
1000Genomes East Asian Sub 1008 T=1.0000 G=0.0000
1000Genomes Europe Sub 1006 T=0.9970 G=0.0030
1000Genomes South Asian Sub 978 T=0.998 G=0.002
1000Genomes American Sub 694 T=0.986 G=0.014
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 T=0.9977 G=0.0023
UK 10K study - Twins TWIN COHORT Study-wide 3708 T=0.9987 G=0.0013
KOREAN population from KRGDB KOREAN Study-wide 2914 T=0.9993 G=0.0007
Genome of the Netherlands Release 5 Genome of the Netherlands Study-wide 998 T=0.999 G=0.001
Medical Genome Project healthy controls from Spanish population Spanish controls Study-wide 534 T=0.993 G=0.007
Northern Sweden ACPOP Study-wide 504 T=0.982 G=0.018
Qatari Global Study-wide 202 T=0.975 G=0.025
SGDP_PRJ Global Study-wide 24 T=0.42 G=0.58
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
GRCh38.p13 chr 1 NC_000001.11:g.25301552= NC_000001.11:g.25301552T>G
GRCh37.p13 chr 1 NC_000001.10:g.25628043= NC_000001.10:g.25628043T>G
RHD RefSeqGene (LRG_796) NG_007494.1:g.34063= NG_007494.1:g.34063T>G
RHD transcript variant 1 NM_016124.4:c.667= NM_016124.4:c.667T>G
RHD transcript variant 1 NM_016124.5:c.667= NM_016124.5:c.667T>G
RHD transcript variant 1 NM_016124.3:c.667= NM_016124.3:c.667T>G
RHD transcript variant 2 NM_001127691.3:c.667= NM_001127691.3:c.667T>G
RHD transcript variant 2 NM_001127691.2:c.667= NM_001127691.2:c.667T>G
RHD transcript variant 2 NM_001127691.1:c.667= NM_001127691.1:c.667T>G
RHD transcript variant 7 NM_001282871.2:c.667= NM_001282871.2:c.667T>G
RHD transcript variant 7 NM_001282871.1:c.667= NM_001282871.1:c.667T>G
RHD transcript variant 5 NM_001282869.2:c.667= NM_001282869.2:c.667T>G
RHD transcript variant 5 NM_001282869.1:c.667= NM_001282869.1:c.667T>G
RHD transcript variant 8 NM_001282872.1:c.667= NM_001282872.1:c.667T>G
RHD transcript variant 3 NM_001282867.1:c.169= NM_001282867.1:c.169T>G
RHD transcript variant 6 NM_001282870.1:c.667= NM_001282870.1:c.667T>G
RHD transcript variant 4 NM_001282868.1:c.667= NM_001282868.1:c.667T>G
RHD transcript variant 2 NM_016225.3:c.667= NM_016225.3:c.667T>G
RHD transcript variant 2 NM_016225.2:c.667= NM_016225.2:c.667T>G
RHD transcript variant X3 XR_946737.2:n.822= XR_946737.2:n.822T>G
RHD transcript variant X1 XM_017002015.1:c.667= XM_017002015.1:c.667T>G
RHD transcript variant X2 XR_946736.1:n.822= XR_946736.1:n.822T>G
LOC51698 transcript NM_016225.1:c.667G>T NM_016225.1:c.667=
blood group Rh(D) polypeptide isoform 1 NP_057208.2:p.Phe223= NP_057208.2:p.Phe223Val
blood group Rh(D) polypeptide isoform 2 NP_001121163.1:p.Phe223= NP_001121163.1:p.Phe223Val
blood group Rh(D) polypeptide isoform 7 NP_001269800.1:p.Phe223= NP_001269800.1:p.Phe223Val
blood group Rh(D) polypeptide isoform 5 NP_001269798.1:p.Phe223= NP_001269798.1:p.Phe223Val
blood group Rh(D) polypeptide isoform 8 NP_001269801.1:p.Phe223= NP_001269801.1:p.Phe223Val
blood group Rh(D) polypeptide isoform 3 NP_001269796.1:p.Phe57= NP_001269796.1:p.Phe57Val
blood group Rh(D) polypeptide isoform 6 NP_001269799.1:p.Phe223= NP_001269799.1:p.Phe223Val
blood group Rh(D) polypeptide isoform 4 NP_001269797.1:p.Phe223= NP_001269797.1:p.Phe223Val
blood group Rh(D) polypeptide isoform X1 XP_016857504.1:p.Phe223= XP_016857504.1:p.Phe223Val
RSRP1 transcript variant 14 NM_001321772.2:c.-67+35488= NM_001321772.2:c.-67+35488A>C
RHD transcript variant X6 XM_005245964.1:c.487-5044= XM_005245964.1:c.487-5044T>G
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, 15 Frequency, 4 ClinVar submissions
No Submitter Submission ID Date (Build)
1 LEE ss4419881 May 29, 2002 (108)
2 1000GENOMES ss328484632 May 09, 2011 (134)
3 1000GENOMES ss489729222 May 04, 2012 (137)
4 EXOME_CHIP ss491289437 May 04, 2012 (137)
5 CLINSEQ_SNP ss491589287 May 04, 2012 (137)
6 NHLBI-ESP ss712285192 Apr 25, 2013 (138)
7 EVA-GONL ss974960337 Aug 21, 2014 (142)
8 JMKIDD_LAB ss1067744291 Aug 21, 2014 (142)
9 1000GENOMES ss1290089410 Aug 21, 2014 (142)
10 DDI ss1425750453 Apr 01, 2015 (144)
11 EVA_UK10K_ALSPAC ss1599754708 Apr 01, 2015 (144)
12 EVA_UK10K_TWINSUK ss1642748741 Apr 01, 2015 (144)
13 EVA_EXAC ss1685398820 Apr 01, 2015 (144)
14 EVA_MGP ss1710896030 Apr 01, 2015 (144)
15 HAMMER_LAB ss1794081808 Sep 08, 2015 (146)
16 WEILL_CORNELL_DGM ss1918172159 Feb 12, 2016 (147)
17 ILLUMINA ss1958254320 Feb 12, 2016 (147)
18 GNOMAD ss2731264816 Nov 08, 2017 (151)
19 GNOMAD ss2746262125 Nov 08, 2017 (151)
20 GNOMAD ss2752823003 Nov 08, 2017 (151)
21 SWEGEN ss2986488866 Nov 08, 2017 (151)
22 ILLUMINA ss3021067979 Nov 08, 2017 (151)
23 TOPMED ss3071294133 Nov 08, 2017 (151)
24 ILLUMINA ss3651393399 Oct 11, 2018 (152)
25 EVA_DECODE ss3686375174 Jul 12, 2019 (153)
26 ACPOP ss3726880701 Jul 12, 2019 (153)
27 KHV_HUMAN_GENOMES ss3798977465 Jul 12, 2019 (153)
28 EVA ss3823579812 Apr 25, 2020 (154)
29 EVA ss3826078502 Apr 25, 2020 (154)
30 SGDP_PRJ ss3848438342 Apr 25, 2020 (154)
31 KRGDB ss3893358186 Apr 25, 2020 (154)
32 EVA ss3986108097 Apr 25, 2021 (155)
33 TOMMO_GENOMICS ss5142995863 Apr 25, 2021 (155)
34 EVA ss5236866394 Apr 25, 2021 (155)
35 1000Genomes NC_000001.10 - 25628043 Oct 11, 2018 (152)
36 The Avon Longitudinal Study of Parents and Children NC_000001.10 - 25628043 Oct 11, 2018 (152)
37 ExAC NC_000001.10 - 25628043 Oct 11, 2018 (152)
38 gnomAD - Genomes NC_000001.11 - 25301552 Apr 25, 2021 (155)
39 gnomAD - Exomes NC_000001.10 - 25628043 Jul 12, 2019 (153)
40 GO Exome Sequencing Project NC_000001.10 - 25628043 Oct 11, 2018 (152)
41 Genome of the Netherlands Release 5 NC_000001.10 - 25628043 Apr 25, 2020 (154)
42 KOREAN population from KRGDB NC_000001.10 - 25628043 Apr 25, 2020 (154)
43 Medical Genome Project healthy controls from Spanish population NC_000001.10 - 25628043 Apr 25, 2020 (154)
44 Northern Sweden NC_000001.10 - 25628043 Jul 12, 2019 (153)
45 Qatari NC_000001.10 - 25628043 Apr 25, 2020 (154)
46 SGDP_PRJ NC_000001.10 - 25628043 Apr 25, 2020 (154)
47 8.3KJPN NC_000001.10 - 25628043 Apr 25, 2021 (155)
48 UK 10K study - Twins NC_000001.10 - 25628043 Oct 11, 2018 (152)
49 ALFA NC_000001.11 - 25301552 Apr 25, 2021 (155)
50 ClinVar RCV000184007.1 Oct 11, 2018 (152)
51 ClinVar RCV000190496.1 Oct 11, 2018 (152)
52 ClinVar RCV000785870.1 Jul 12, 2019 (153)
53 ClinVar RCV000785871.1 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).

Associated ID History Updated (Build)
rs3193871 Oct 09, 2002 (108)
Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
ss491589287 NC_000001.9:25500629:T:G NC_000001.11:25301551:T:G (self)
779381, 414712, 4584528, 278757, 38515, 179763, 535580, 12782, 165566, 214089, 455322, 965170, 414712, ss328484632, ss489729222, ss491289437, ss712285192, ss974960337, ss1067744291, ss1290089410, ss1425750453, ss1599754708, ss1642748741, ss1685398820, ss1710896030, ss1794081808, ss1918172159, ss1958254320, ss2731264816, ss2746262125, ss2752823003, ss2986488866, ss3021067979, ss3651393399, ss3726880701, ss3823579812, ss3826078502, ss3848438342, ss3893358186, ss3986108097, ss5142995863 NC_000001.10:25628042:T:G NC_000001.11:25301551:T:G (self)
RCV000184007.1, RCV000190496.1, RCV000785870.1, RCV000785871.1, 5448861, 13048196508, ss3071294133, ss3686375174, ss3798977465, ss5236866394 NC_000001.11:25301551:T:G NC_000001.11:25301551:T:G (self)
ss4419881 NT_004610.19:12308130:T:G NC_000001.11:25301551: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 rs1053356
PMID Title Author Year Journal
24579654 How do we identify RHD variants using a practical molecular approach? Arnoni CP et al. 2014 Transfusion
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