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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.

rs375471538

Current Build 155

Released April 9, 2021

Organism
Homo sapiens
Position
chr1:25321961 (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
A>T
Variation Type
SNV Single Nucleotide Variation
Frequency
T=0.000004 (1/264690, TOPMED)
T=0.000009 (2/224158, GnomAD_exome)
T=0.000025 (3/122008, GnomAD) (+ 3 more)
T=0.000009 (1/105480, ExAC)
T=0.00014 (2/14050, ALFA)
T=0.00009 (1/11662, GO-ESP)
Clinical Significance
Not 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.25321961A>T
GRCh37.p13 chr 1 NC_000001.10:g.25648452A>T
RHD RefSeqGene (LRG_796) NG_007494.1:g.54472A>T
Gene: RHD, Rh blood group D antigen (plus strand)
Molecule type Change Amino acid[Codon] SO Term
RHD transcript variant 2 NM_001127691.3:c.940-6937…

NM_001127691.3:c.940-6937A>T

N/A Intron Variant
RHD transcript variant 4 NM_001282868.1:c.1019+488…

NM_001282868.1:c.1019+4882A>T

N/A Intron Variant
RHD transcript variant 5 NM_001282869.2:c.1074-693…

NM_001282869.2:c.1074-6937A>T

N/A Intron Variant
RHD transcript variant 6 NM_001282870.1:c.1153+488…

NM_001282870.1:c.1153+4882A>T

N/A Intron Variant
RHD transcript variant 7 NM_001282871.2:c.1244-693…

NM_001282871.2:c.1244-6937A>T

N/A Intron Variant
RHD transcript variant 8 NM_001282872.1:c.*27+4882…

NM_001282872.1:c.*27+4882A>T

N/A Intron Variant
RHD transcript variant 3 NM_001282867.1:c.728A>T K [AAG] > M [ATG] Coding Sequence Variant
blood group Rh(D) polypeptide isoform 3 NP_001269796.1:p.Lys243Met K (Lys) > M (Met) Missense Variant
RHD transcript variant 1 NM_016124.5:c.1226A>T K [AAG] > M [ATG] Coding Sequence Variant
blood group Rh(D) polypeptide isoform 1 NP_057208.2:p.Lys409Met K (Lys) > M (Met) Missense Variant
RHD transcript variant X1 XM_017002015.1:c. N/A Genic Downstream Transcript Variant
RHD transcript variant X2 XR_946736.1:n.1301A>T N/A Non Coding Transcript Variant
RHD transcript variant X3 XR_946737.2:n.1247A>T N/A Non Coding Transcript Variant
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+1507…

NM_001321772.2:c.-67+15079T>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 18 NR_135790.1:n. N/A Intron Variant
RSRP1 transcript variant 19 NR_135791.1:n. N/A Intron Variant
RSRP1 transcript variant 20 NR_135792.1:n. N/A Intron Variant
RSRP1 transcript variant 21 NR_135793.1: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 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
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

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 14050 A=0.99986 T=0.00014
European Sub 9690 A=0.9998 T=0.0002
African Sub 2898 A=1.0000 T=0.0000
African Others Sub 114 A=1.000 T=0.000
African American Sub 2784 A=1.0000 T=0.0000
Asian Sub 112 A=1.000 T=0.000
East Asian Sub 86 A=1.00 T=0.00
Other Asian Sub 26 A=1.00 T=0.00
Latin American 1 Sub 146 A=1.000 T=0.000
Latin American 2 Sub 610 A=1.000 T=0.000
South Asian Sub 98 A=1.00 T=0.00
Other Sub 496 A=1.000 T=0.000


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=0.999996 T=0.000004
gnomAD - Exomes Global Study-wide 224158 A=0.999991 T=0.000009
gnomAD - Exomes European Sub 114026 A=0.999982 T=0.000018
gnomAD - Exomes Asian Sub 46922 A=1.00000 T=0.00000
gnomAD - Exomes American Sub 33002 A=1.00000 T=0.00000
gnomAD - Exomes African Sub 15622 A=1.00000 T=0.00000
gnomAD - Exomes Ashkenazi Jewish Sub 9158 A=1.0000 T=0.0000
gnomAD - Exomes Other Sub 5428 A=1.0000 T=0.0000
gnomAD - Genomes Global Study-wide 122008 A=0.999975 T=0.000025
gnomAD - Genomes European Sub 62392 A=0.99995 T=0.00005
gnomAD - Genomes African Sub 39480 A=1.00000 T=0.00000
gnomAD - Genomes American Sub 12150 A=1.00000 T=0.00000
gnomAD - Genomes East Asian Sub 3112 A=1.0000 T=0.0000
gnomAD - Genomes Ashkenazi Jewish Sub 3004 A=1.0000 T=0.0000
gnomAD - Genomes Other Sub 1870 A=1.0000 T=0.0000
ExAC Global Study-wide 105480 A=0.999991 T=0.000009
ExAC Europe Sub 60366 A=0.99998 T=0.00002
ExAC Asian Sub 23670 A=1.00000 T=0.00000
ExAC American Sub 10916 A=1.00000 T=0.00000
ExAC African Sub 9706 A=1.0000 T=0.0000
ExAC Other Sub 822 A=1.000 T=0.000
Allele Frequency Aggregator Total Global 14050 A=0.99986 T=0.00014
Allele Frequency Aggregator European Sub 9690 A=0.9998 T=0.0002
Allele Frequency Aggregator African Sub 2898 A=1.0000 T=0.0000
Allele Frequency Aggregator Latin American 2 Sub 610 A=1.000 T=0.000
Allele Frequency Aggregator Other Sub 496 A=1.000 T=0.000
Allele Frequency Aggregator Latin American 1 Sub 146 A=1.000 T=0.000
Allele Frequency Aggregator Asian Sub 112 A=1.000 T=0.000
Allele Frequency Aggregator South Asian Sub 98 A=1.00 T=0.00
GO Exome Sequencing Project Global Study-wide 11662 A=0.99991 T=0.00009
GO Exome Sequencing Project European American Sub 7400 A=0.9999 T=0.0001
GO Exome Sequencing Project African American Sub 4262 A=1.0000 T=0.0000
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= T
GRCh38.p13 chr 1 NC_000001.11:g.25321961= NC_000001.11:g.25321961A>T
GRCh37.p13 chr 1 NC_000001.10:g.25648452= NC_000001.10:g.25648452A>T
RHD RefSeqGene (LRG_796) NG_007494.1:g.54472= NG_007494.1:g.54472A>T
RHD transcript variant 1 NM_016124.4:c.1226= NM_016124.4:c.1226A>T
RHD transcript variant 1 NM_016124.5:c.1226= NM_016124.5:c.1226A>T
RHD transcript variant 1 NM_016124.3:c.1226= NM_016124.3:c.1226A>T
RHD transcript variant 3 NM_001282867.1:c.728= NM_001282867.1:c.728A>T
RHD transcript variant 2 NM_016225.3:c.*61= NM_016225.3:c.*61A>T
RHD transcript variant 2 NM_016225.2:c.*61= NM_016225.2:c.*61A>T
RHD transcript variant X3 XR_946737.2:n.1247= XR_946737.2:n.1247A>T
RHD transcript variant X2 XR_946736.1:n.1301= XR_946736.1:n.1301A>T
LOC51698 transcript NM_016225.1:c.1226= NM_016225.1:c.1226A>T
blood group Rh(D) polypeptide isoform 1 NP_057208.2:p.Lys409= NP_057208.2:p.Lys409Met
blood group Rh(D) polypeptide isoform 3 NP_001269796.1:p.Lys243= NP_001269796.1:p.Lys243Met
RHD transcript variant 2 NM_001127691.1:c.940-6937= NM_001127691.1:c.940-6937A>T
RHD transcript variant 2 NM_001127691.3:c.940-6937= NM_001127691.3:c.940-6937A>T
RHD transcript variant 4 NM_001282868.1:c.1019+4882= NM_001282868.1:c.1019+4882A>T
RHD transcript variant 5 NM_001282869.2:c.1074-6937= NM_001282869.2:c.1074-6937A>T
RHD transcript variant 6 NM_001282870.1:c.1153+4882= NM_001282870.1:c.1153+4882A>T
RHD transcript variant 7 NM_001282871.2:c.1244-6937= NM_001282871.2:c.1244-6937A>T
RHD transcript variant 8 NM_001282872.1:c.*27+4882= NM_001282872.1:c.*27+4882A>T
RSRP1 transcript variant 14 NM_001321772.2:c.-67+15079= NM_001321772.2:c.-67+15079T>A
RHD transcript variant X1 XM_005245959.1:c.1244-6937= XM_005245959.1:c.1244-6937A>T
RHD transcript variant X2 XM_005245960.1:c.1153+4882= XM_005245960.1:c.1153+4882A>T
RHD transcript variant X3 XM_005245961.1:c.*27+4882= XM_005245961.1:c.*27+4882A>T
RHD transcript variant X4 XM_005245962.1:c.1074-6937= XM_005245962.1:c.1074-6937A>T
RHD transcript variant X5 XM_005245963.1:c.1019+4882= XM_005245963.1:c.1019+4882A>T
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#.

8 SubSNP, 6 Frequency submissions
No Submitter Submission ID Date (Build)
1 NHLBI-ESP ss712285216 Apr 25, 2013 (138)
2 EVA_EXAC ss1685399007 Apr 01, 2015 (144)
3 GNOMAD ss2731265128 Nov 08, 2017 (151)
4 GNOMAD ss2746262231 Nov 08, 2017 (151)
5 GNOMAD ss2752824692 Nov 08, 2017 (151)
6 TOPMED ss3071297779 Nov 08, 2017 (151)
7 EVA ss3823579857 Apr 25, 2020 (154)
8 TOPMED ss4442607223 Apr 25, 2021 (155)
9 ExAC NC_000001.10 - 25648452 Oct 11, 2018 (152)
10 gnomAD - Genomes NC_000001.11 - 25321961 Apr 25, 2021 (155)
11 gnomAD - Exomes NC_000001.10 - 25648452 Jul 12, 2019 (153)
12 GO Exome Sequencing Project NC_000001.10 - 25648452 Oct 11, 2018 (152)
13 TopMed NC_000001.11 - 25321961 Apr 25, 2021 (155)
14 ALFA NC_000001.11 - 25321961 Apr 25, 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
4584724, 279092, 38559, ss712285216, ss1685399007, ss2731265128, ss2746262231, ss2752824692, ss3823579857 NC_000001.10:25648451:A:T NC_000001.11:25321960:A:T (self)
5452358, 3908100, 6213558, 620744495, ss3071297779, ss4442607223 NC_000001.11:25321960:A:T NC_000001.11:25321960:A: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 rs375471538

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