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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.

rs41300142

Current Build 155

Released April 9, 2021

Organism
Homo sapiens
Position
chr1:25306709 (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
C>A / C>T
Variation Type
SNV Single Nucleotide Variation
Frequency
T=0.000341 (41/120276, GnomAD)
T=0.00034 (4/11862, ALFA)
A=0.00017 (2/11732, GO-ESP) (+ 1 more)
T=0.0002 (1/5008, 1000G)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
RHD : Synonymous Variant
RSRP1 : Non Coding Transcript 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.25306709C>A
GRCh38.p13 chr 1 NC_000001.11:g.25306709C>T
GRCh37.p13 chr 1 NC_000001.10:g.25633200C>A
GRCh37.p13 chr 1 NC_000001.10:g.25633200C>T
RHD RefSeqGene (LRG_796) NG_007494.1:g.39220C>A
RHD RefSeqGene (LRG_796) NG_007494.1:g.39220C>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.939+3250…

NM_001127691.3:c.939+3250C>A

N/A Intron Variant
RHD transcript variant 4 NM_001282868.1:c.939+3250…

NM_001282868.1:c.939+3250C>A

N/A Intron Variant
RHD transcript variant 3 NM_001282867.1:c.555C>A T [ACC] > T [ACA] Coding Sequence Variant
blood group Rh(D) polypeptide isoform 3 NP_001269796.1:p.Thr185= T (Thr) > T (Thr) Synonymous Variant
RHD transcript variant 3 NM_001282867.1:c.555C>T T [ACC] > T [ACT] Coding Sequence Variant
blood group Rh(D) polypeptide isoform 3 NP_001269796.1:p.Thr185= T (Thr) > T (Thr) Synonymous Variant
RHD transcript variant 6 NM_001282870.1:c.1053C>A T [ACC] > T [ACA] Coding Sequence Variant
blood group Rh(D) polypeptide isoform 6 NP_001269799.1:p.Thr351= T (Thr) > T (Thr) Synonymous Variant
RHD transcript variant 6 NM_001282870.1:c.1053C>T T [ACC] > T [ACT] Coding Sequence Variant
blood group Rh(D) polypeptide isoform 6 NP_001269799.1:p.Thr351= T (Thr) > T (Thr) Synonymous Variant
RHD transcript variant 8 NM_001282872.1:c.1053C>A T [ACC] > T [ACA] Coding Sequence Variant
blood group Rh(D) polypeptide isoform 8 NP_001269801.1:p.Thr351= T (Thr) > T (Thr) Synonymous Variant
RHD transcript variant 8 NM_001282872.1:c.1053C>T T [ACC] > T [ACT] Coding Sequence Variant
blood group Rh(D) polypeptide isoform 8 NP_001269801.1:p.Thr351= T (Thr) > T (Thr) Synonymous Variant
RHD transcript variant 5 NM_001282869.2:c.1053C>A T [ACC] > T [ACA] Coding Sequence Variant
blood group Rh(D) polypeptide isoform 5 NP_001269798.1:p.Thr351= T (Thr) > T (Thr) Synonymous Variant
RHD transcript variant 5 NM_001282869.2:c.1053C>T T [ACC] > T [ACT] Coding Sequence Variant
blood group Rh(D) polypeptide isoform 5 NP_001269798.1:p.Thr351= T (Thr) > T (Thr) Synonymous Variant
RHD transcript variant 7 NM_001282871.2:c.1053C>A T [ACC] > T [ACA] Coding Sequence Variant
blood group Rh(D) polypeptide isoform 7 NP_001269800.1:p.Thr351= T (Thr) > T (Thr) Synonymous Variant
RHD transcript variant 7 NM_001282871.2:c.1053C>T T [ACC] > T [ACT] Coding Sequence Variant
blood group Rh(D) polypeptide isoform 7 NP_001269800.1:p.Thr351= T (Thr) > T (Thr) Synonymous Variant
RHD transcript variant 1 NM_016124.5:c.1053C>A T [ACC] > T [ACA] Coding Sequence Variant
blood group Rh(D) polypeptide isoform 1 NP_057208.2:p.Thr351= T (Thr) > T (Thr) Synonymous Variant
RHD transcript variant 1 NM_016124.5:c.1053C>T T [ACC] > T [ACT] Coding Sequence Variant
blood group Rh(D) polypeptide isoform 1 NP_057208.2:p.Thr351= T (Thr) > T (Thr) Synonymous Variant
RHD transcript variant X1 XM_017002015.1:c.1053C>A T [ACC] > T [ACA] Coding Sequence Variant
blood group Rh(D) polypeptide isoform X1 XP_016857504.1:p.Thr351= T (Thr) > T (Thr) Synonymous Variant
RHD transcript variant X1 XM_017002015.1:c.1053C>T T [ACC] > T [ACT] Coding Sequence Variant
blood group Rh(D) polypeptide isoform X1 XP_016857504.1:p.Thr351= T (Thr) > T (Thr) Synonymous Variant
RHD transcript variant X2 XR_946736.1:n.1208C>A N/A Non Coding Transcript Variant
RHD transcript variant X2 XR_946736.1:n.1208C>T N/A Non Coding Transcript Variant
RHD transcript variant X3 XR_946737.2:n. N/A Intron 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+3033…

NM_001321772.2:c.-67+30331G>T

N/A Intron Variant
RSRP1 transcript variant 2 NM_020317.5:c. N/A Genic Upstream Transcript Variant
RSRP1 transcript variant 19 NR_135791.1:n.1456G>T N/A Non Coding Transcript Variant
RSRP1 transcript variant 19 NR_135791.1:n.1456G>A N/A Non Coding 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 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 11862 C=0.99966 T=0.00034
European Sub 7618 C=0.9999 T=0.0001
African Sub 2816 C=0.9989 T=0.0011
African Others Sub 108 C=1.000 T=0.000
African American Sub 2708 C=0.9989 T=0.0011
Asian Sub 108 C=1.000 T=0.000
East Asian Sub 84 C=1.00 T=0.00
Other Asian Sub 24 C=1.00 T=0.00
Latin American 1 Sub 146 C=1.000 T=0.000
Latin American 2 Sub 610 C=1.000 T=0.000
South Asian Sub 94 C=1.00 T=0.00
Other Sub 470 C=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
gnomAD - Genomes Global Study-wide 120276 C=0.999659 T=0.000341
gnomAD - Genomes European Sub 61904 C=0.99997 T=0.00003
gnomAD - Genomes African Sub 38388 C=0.99917 T=0.00083
gnomAD - Genomes American Sub 12036 C=1.00000 T=0.00000
gnomAD - Genomes East Asian Sub 3118 C=1.0000 T=0.0000
gnomAD - Genomes Ashkenazi Jewish Sub 2988 C=0.9977 T=0.0023
gnomAD - Genomes Other Sub 1842 C=1.0000 T=0.0000
GO Exome Sequencing Project Global Study-wide 11732 C=0.99983 A=0.00017
GO Exome Sequencing Project European American Sub 7504 C=1.0000 A=0.0000
GO Exome Sequencing Project African American Sub 4228 C=0.9995 A=0.0005
1000Genomes Global Study-wide 5008 C=0.9998 T=0.0002
1000Genomes African Sub 1322 C=0.9992 T=0.0008
1000Genomes East Asian Sub 1008 C=1.0000 T=0.0000
1000Genomes Europe Sub 1006 C=1.0000 T=0.0000
1000Genomes South Asian Sub 978 C=1.000 T=0.000
1000Genomes American Sub 694 C=1.000 T=0.000
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 C= A T
GRCh38.p13 chr 1 NC_000001.11:g.25306709= NC_000001.11:g.25306709C>A NC_000001.11:g.25306709C>T
GRCh37.p13 chr 1 NC_000001.10:g.25633200= NC_000001.10:g.25633200C>A NC_000001.10:g.25633200C>T
RHD RefSeqGene (LRG_796) NG_007494.1:g.39220= NG_007494.1:g.39220C>A NG_007494.1:g.39220C>T
RHD transcript variant 1 NM_016124.4:c.1053= NM_016124.4:c.1053C>A NM_016124.4:c.1053C>T
RHD transcript variant 1 NM_016124.5:c.1053= NM_016124.5:c.1053C>A NM_016124.5:c.1053C>T
RHD transcript variant 1 NM_016124.3:c.1053= NM_016124.3:c.1053C>A NM_016124.3:c.1053C>T
RHD transcript variant 7 NM_001282871.2:c.1053= NM_001282871.2:c.1053C>A NM_001282871.2:c.1053C>T
RHD transcript variant 7 NM_001282871.1:c.1053= NM_001282871.1:c.1053C>A NM_001282871.1:c.1053C>T
RHD transcript variant 5 NM_001282869.2:c.1053= NM_001282869.2:c.1053C>A NM_001282869.2:c.1053C>T
RHD transcript variant 5 NM_001282869.1:c.1053= NM_001282869.1:c.1053C>A NM_001282869.1:c.1053C>T
RHD transcript variant 8 NM_001282872.1:c.1053= NM_001282872.1:c.1053C>A NM_001282872.1:c.1053C>T
RHD transcript variant 3 NM_001282867.1:c.555= NM_001282867.1:c.555C>A NM_001282867.1:c.555C>T
RHD transcript variant 6 NM_001282870.1:c.1053= NM_001282870.1:c.1053C>A NM_001282870.1:c.1053C>T
RSRP1 transcript variant 19 NR_135791.1:n.1456= NR_135791.1:n.1456G>T NR_135791.1:n.1456G>A
RHD transcript variant X1 XM_017002015.1:c.1053= XM_017002015.1:c.1053C>A XM_017002015.1:c.1053C>T
RHD transcript variant X2 XR_946736.1:n.1208= XR_946736.1:n.1208C>A XR_946736.1:n.1208C>T
LOC51698 transcript NM_016225.1:c.1053= NM_016225.1:c.1053C>A NM_016225.1:c.1053C>T
blood group Rh(D) polypeptide isoform 1 NP_057208.2:p.Thr351= NP_057208.2:p.Thr351= NP_057208.2:p.Thr351=
blood group Rh(D) polypeptide isoform 7 NP_001269800.1:p.Thr351= NP_001269800.1:p.Thr351= NP_001269800.1:p.Thr351=
blood group Rh(D) polypeptide isoform 5 NP_001269798.1:p.Thr351= NP_001269798.1:p.Thr351= NP_001269798.1:p.Thr351=
blood group Rh(D) polypeptide isoform 8 NP_001269801.1:p.Thr351= NP_001269801.1:p.Thr351= NP_001269801.1:p.Thr351=
blood group Rh(D) polypeptide isoform 3 NP_001269796.1:p.Thr185= NP_001269796.1:p.Thr185= NP_001269796.1:p.Thr185=
blood group Rh(D) polypeptide isoform 6 NP_001269799.1:p.Thr351= NP_001269799.1:p.Thr351= NP_001269799.1:p.Thr351=
blood group Rh(D) polypeptide isoform X1 XP_016857504.1:p.Thr351= XP_016857504.1:p.Thr351= XP_016857504.1:p.Thr351=
RHD transcript variant 2 NM_001127691.1:c.939+3250= NM_001127691.1:c.939+3250C>A NM_001127691.1:c.939+3250C>T
RHD transcript variant 2 NM_001127691.3:c.939+3250= NM_001127691.3:c.939+3250C>A NM_001127691.3:c.939+3250C>T
RHD transcript variant 4 NM_001282868.1:c.939+3250= NM_001282868.1:c.939+3250C>A NM_001282868.1:c.939+3250C>T
RSRP1 transcript variant 14 NM_001321772.2:c.-67+30331= NM_001321772.2:c.-67+30331G>T NM_001321772.2:c.-67+30331G>A
RHD transcript variant X5 XM_005245963.1:c.939+3250= XM_005245963.1:c.939+3250C>A XM_005245963.1:c.939+3250C>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#.

10 SubSNP, 8 Frequency submissions
No Submitter Submission ID Date (Build)
1 SI_EXO ss61705141 Oct 18, 2006 (127)
2 NHLBI-ESP ss712285207 Apr 25, 2013 (138)
3 1000GENOMES ss1290089579 Aug 21, 2014 (142)
4 EVA_EXAC ss1685398940 Apr 01, 2015 (144)
5 EVA_EXAC ss1685398941 Apr 01, 2015 (144)
6 GNOMAD ss2731264996 Nov 08, 2017 (151)
7 GNOMAD ss2746262181 Nov 08, 2017 (151)
8 GNOMAD ss2752823452 Nov 08, 2017 (151)
9 TOPMED ss3071295059 Nov 08, 2017 (151)
10 EVA ss3823579845 Apr 25, 2020 (154)
11 1000Genomes NC_000001.10 - 25633200 Oct 11, 2018 (152)
12 ExAC

Submission ignored due to conflicting rows:
Row 4584651 (NC_000001.10:25633199:C:C 108257/108264, NC_000001.10:25633199:C:T 7/108264)
Row 4584652 (NC_000001.10:25633199:C:C 108262/108264, NC_000001.10:25633199:C:A 2/108264)

- Oct 11, 2018 (152)
13 ExAC

Submission ignored due to conflicting rows:
Row 4584651 (NC_000001.10:25633199:C:C 108257/108264, NC_000001.10:25633199:C:T 7/108264)
Row 4584652 (NC_000001.10:25633199:C:C 108262/108264, NC_000001.10:25633199:C:A 2/108264)

- Oct 11, 2018 (152)
14 gnomAD - Genomes NC_000001.11 - 25306709 Apr 25, 2021 (155)
15 gnomAD - Exomes

Submission ignored due to conflicting rows:
Row 278942 (NC_000001.10:25633199:C:C 225102/225104, NC_000001.10:25633199:C:A 2/225104)
Row 278943 (NC_000001.10:25633199:C:C 225083/225104, NC_000001.10:25633199:C:T 21/225104)

- Jul 12, 2019 (153)
16 gnomAD - Exomes

Submission ignored due to conflicting rows:
Row 278942 (NC_000001.10:25633199:C:C 225102/225104, NC_000001.10:25633199:C:A 2/225104)
Row 278943 (NC_000001.10:25633199:C:C 225083/225104, NC_000001.10:25633199:C:T 21/225104)

- Jul 12, 2019 (153)
17 GO Exome Sequencing Project NC_000001.10 - 25633200 Oct 11, 2018 (152)
18 ALFA NC_000001.11 - 25306709 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
38547, ss712285207, ss1685398941, ss2731264996, ss3823579845 NC_000001.10:25633199:C:A NC_000001.11:25306708:C:A (self)
779559, ss1290089579, ss1685398940, ss2731264996, ss2746262181, ss2752823452 NC_000001.10:25633199:C:T NC_000001.11:25306708:C:T (self)
5449798, 6184807275, ss3071295059 NC_000001.11:25306708:C:T NC_000001.11:25306708:C:T (self)
ss61705141 NT_004610.17:8457551:C:T NC_000001.11:25306708:C: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 rs41300142

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