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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.

rs10801171

Current Build 155

Released April 9, 2021

Organism
Homo sapiens
Position
chr1:193073886 (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>G / C>T
Variation Type
SNV Single Nucleotide Variation
Frequency
G=0.326790 (86498/264690, TOPMED)
A=0.000103 (12/117070, GnomAD)
G=0.44131 (7369/16698, 8.3KJPN) (+ 6 more)
G=0.1934 (1882/9730, ALFA)
G=0.3065 (1535/5008, 1000G)
G=0.3505 (1027/2930, KOREAN)
G=0.3377 (616/1824, Korea1K)
C=0.335 (114/340, SGDP_PRJ)
G=0.301 (65/216, Qatari)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
RO60 : 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.193073886C>A
GRCh38.p13 chr 1 NC_000001.11:g.193073886C>G
GRCh38.p13 chr 1 NC_000001.11:g.193073886C>T
GRCh37.p13 chr 1 NC_000001.10:g.193043016C>A
GRCh37.p13 chr 1 NC_000001.10:g.193043016C>G
GRCh37.p13 chr 1 NC_000001.10:g.193043016C>T
Gene: RO60, Ro60, Y RNA binding protein (plus strand)
Molecule type Change Amino acid[Codon] SO Term
RO60 transcript variant 1 NM_001042369.2:c.581-1934…

NM_001042369.2:c.581-1934C>A

N/A Intron Variant
RO60 transcript variant 3 NM_001042370.2:c.581-1934…

NM_001042370.2:c.581-1934C>A

N/A Intron Variant
RO60 transcript variant 5 NM_001173524.2:c.581-1934…

NM_001173524.2:c.581-1934C>A

N/A Intron Variant
RO60 transcript variant 4 NM_001173525.1:c.581-1934…

NM_001173525.1:c.581-1934C>A

N/A Intron Variant
RO60 transcript variant 6 NM_001331020.2:c.-245-193…

NM_001331020.2:c.-245-1934C>A

N/A Intron Variant
RO60 transcript variant 2 NM_004600.5:c.581-1934C>A N/A Intron Variant
RO60 transcript variant X1 XM_006711495.4:c.647-1934…

XM_006711495.4:c.647-1934C>A

N/A Intron Variant
RO60 transcript variant X2 XM_006711496.3:c.647-1934…

XM_006711496.3:c.647-1934C>A

N/A Intron Variant
RO60 transcript variant X4 XM_006711497.3:c.581-1934…

XM_006711497.3:c.581-1934C>A

N/A Intron Variant
RO60 transcript variant X8 XM_011509922.2:c.-245-193…

XM_011509922.2:c.-245-1934C>A

N/A Intron Variant
RO60 transcript variant X3 XM_017002180.1:c.647-1934…

XM_017002180.1:c.647-1934C>A

N/A Intron Variant
RO60 transcript variant X5 XM_017002181.2:c.581-1934…

XM_017002181.2:c.581-1934C>A

N/A Intron Variant
RO60 transcript variant X6 XM_017002182.1:c.581-1934…

XM_017002182.1:c.581-1934C>A

N/A Intron Variant
RO60 transcript variant X9 XM_017002183.1:c.-24-2615…

XM_017002183.1:c.-24-2615C>A

N/A Intron Variant
RO60 transcript variant X7 XM_024449332.1:c.581-1934…

XM_024449332.1:c.581-1934C>A

N/A Intron 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 9730 C=0.8066 A=0.0000, G=0.1934, T=0.0000
European Sub 6816 C=0.7245 A=0.0000, G=0.2755, T=0.0000
African Sub 2374 C=1.0000 A=0.0000, G=0.0000, T=0.0000
African Others Sub 108 C=1.000 A=0.000, G=0.000, T=0.000
African American Sub 2266 C=1.0000 A=0.0000, G=0.0000, T=0.0000
Asian Sub 34 C=1.00 A=0.00, G=0.00, T=0.00
East Asian Sub 26 C=1.00 A=0.00, G=0.00, T=0.00
Other Asian Sub 8 C=1.0 A=0.0, G=0.0, T=0.0
Latin American 1 Sub 68 C=1.00 A=0.00, G=0.00, T=0.00
Latin American 2 Sub 206 C=1.000 A=0.000, G=0.000, T=0.000
South Asian Sub 24 C=1.00 A=0.00, G=0.00, T=0.00
Other Sub 208 C=0.981 A=0.000, G=0.019, 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 C=0.673210 G=0.326790
gnomAD - Genomes Global Study-wide 117070 C=0.999897 A=0.000103
gnomAD - Genomes European Sub 68298 C=1.00000 A=0.00000
gnomAD - Genomes African Sub 30096 C=0.99967 A=0.00033
gnomAD - Genomes American Sub 11132 C=0.99982 A=0.00018
gnomAD - Genomes Ashkenazi Jewish Sub 3074 C=1.0000 A=0.0000
gnomAD - Genomes East Asian Sub 2732 C=1.0000 A=0.0000
gnomAD - Genomes Other Sub 1738 C=1.0000 A=0.0000
8.3KJPN JAPANESE Study-wide 16698 C=0.55869 G=0.44131
1000Genomes Global Study-wide 5008 C=0.6935 G=0.3065
1000Genomes African Sub 1322 C=0.9750 G=0.0250
1000Genomes East Asian Sub 1008 C=0.6577 G=0.3423
1000Genomes Europe Sub 1006 C=0.6034 G=0.3966
1000Genomes South Asian Sub 978 C=0.495 G=0.505
1000Genomes American Sub 694 C=0.620 G=0.380
KOREAN population from KRGDB KOREAN Study-wide 2930 C=0.6495 G=0.3505
Korean Genome Project KOREAN Study-wide 1824 C=0.6623 G=0.3377
SGDP_PRJ Global Study-wide 340 C=0.335 G=0.665
Qatari Global Study-wide 216 C=0.699 G=0.301
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 G T
GRCh38.p13 chr 1 NC_000001.11:g.193073886= NC_000001.11:g.193073886C>A NC_000001.11:g.193073886C>G NC_000001.11:g.193073886C>T
GRCh37.p13 chr 1 NC_000001.10:g.193043016= NC_000001.10:g.193043016C>A NC_000001.10:g.193043016C>G NC_000001.10:g.193043016C>T
RO60 transcript variant 1 NM_001042369.2:c.581-1934= NM_001042369.2:c.581-1934C>A NM_001042369.2:c.581-1934C>G NM_001042369.2:c.581-1934C>T
RO60 transcript variant 3 NM_001042370.2:c.581-1934= NM_001042370.2:c.581-1934C>A NM_001042370.2:c.581-1934C>G NM_001042370.2:c.581-1934C>T
RO60 transcript variant 5 NM_001173524.1:c.581-1934= NM_001173524.1:c.581-1934C>A NM_001173524.1:c.581-1934C>G NM_001173524.1:c.581-1934C>T
RO60 transcript variant 5 NM_001173524.2:c.581-1934= NM_001173524.2:c.581-1934C>A NM_001173524.2:c.581-1934C>G NM_001173524.2:c.581-1934C>T
RO60 transcript variant 4 NM_001173525.1:c.581-1934= NM_001173525.1:c.581-1934C>A NM_001173525.1:c.581-1934C>G NM_001173525.1:c.581-1934C>T
RO60 transcript variant 6 NM_001331020.2:c.-245-1934= NM_001331020.2:c.-245-1934C>A NM_001331020.2:c.-245-1934C>G NM_001331020.2:c.-245-1934C>T
RO60 transcript variant 2 NM_004600.5:c.581-1934= NM_004600.5:c.581-1934C>A NM_004600.5:c.581-1934C>G NM_004600.5:c.581-1934C>T
RO60 transcript variant X1 XM_006711495.4:c.647-1934= XM_006711495.4:c.647-1934C>A XM_006711495.4:c.647-1934C>G XM_006711495.4:c.647-1934C>T
RO60 transcript variant X2 XM_006711496.3:c.647-1934= XM_006711496.3:c.647-1934C>A XM_006711496.3:c.647-1934C>G XM_006711496.3:c.647-1934C>T
RO60 transcript variant X4 XM_006711497.3:c.581-1934= XM_006711497.3:c.581-1934C>A XM_006711497.3:c.581-1934C>G XM_006711497.3:c.581-1934C>T
RO60 transcript variant X8 XM_011509922.2:c.-245-1934= XM_011509922.2:c.-245-1934C>A XM_011509922.2:c.-245-1934C>G XM_011509922.2:c.-245-1934C>T
RO60 transcript variant X3 XM_017002180.1:c.647-1934= XM_017002180.1:c.647-1934C>A XM_017002180.1:c.647-1934C>G XM_017002180.1:c.647-1934C>T
RO60 transcript variant X5 XM_017002181.2:c.581-1934= XM_017002181.2:c.581-1934C>A XM_017002181.2:c.581-1934C>G XM_017002181.2:c.581-1934C>T
RO60 transcript variant X6 XM_017002182.1:c.581-1934= XM_017002182.1:c.581-1934C>A XM_017002182.1:c.581-1934C>G XM_017002182.1:c.581-1934C>T
RO60 transcript variant X9 XM_017002183.1:c.-24-2615= XM_017002183.1:c.-24-2615C>A XM_017002183.1:c.-24-2615C>G XM_017002183.1:c.-24-2615C>T
RO60 transcript variant X7 XM_024449332.1:c.581-1934= XM_024449332.1:c.581-1934C>A XM_024449332.1:c.581-1934C>G XM_024449332.1:c.581-1934C>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#.

29 SubSNP, 9 Frequency submissions
No Submitter Submission ID Date (Build)
1 CSHL-HAPMAP ss17324211 Feb 27, 2004 (120)
2 SC_SNP ss18069715 Feb 27, 2004 (120)
3 SC_SNP ss18243017 Feb 27, 2004 (120)
4 ABI ss41084957 Mar 13, 2006 (126)
5 BCMHGSC_JDW ss87916062 Mar 23, 2008 (129)
6 BCM-HGSC-SUB ss205506440 Jul 04, 2010 (132)
7 GMI ss276153451 May 04, 2012 (137)
8 GMI ss284199340 Apr 25, 2013 (138)
9 PJP ss290691832 May 09, 2011 (134)
10 SSMP ss648589786 Apr 25, 2013 (138)
11 1000GENOMES ss1293994286 Aug 21, 2014 (142)
12 DDI ss1426060977 Apr 01, 2015 (144)
13 WEILL_CORNELL_DGM ss1919200008 Feb 12, 2016 (147)
14 GRF ss2698132077 Nov 08, 2017 (151)
15 GNOMAD ss2764351809 Nov 08, 2017 (151)
16 SWEGEN ss2988180482 Nov 08, 2017 (151)
17 TOPMED ss3099104670 Nov 08, 2017 (151)
18 TOPMED ss3099104671 Nov 08, 2017 (151)
19 TOPMED ss3099104672 Nov 08, 2017 (151)
20 CSHL ss3343835073 Nov 08, 2017 (151)
21 URBANLAB ss3646850174 Oct 11, 2018 (152)
22 EVA_DECODE ss3688302637 Jul 12, 2019 (153)
23 KHV_HUMAN_GENOMES ss3800138142 Jul 12, 2019 (153)
24 EVA ss3826560933 Apr 25, 2020 (154)
25 SGDP_PRJ ss3850557515 Apr 25, 2020 (154)
26 KRGDB ss3895832248 Apr 25, 2020 (154)
27 KOGIC ss3946167428 Apr 25, 2020 (154)
28 TOPMED ss4477773114 Apr 25, 2021 (155)
29 TOMMO_GENOMICS ss5147685512 Apr 25, 2021 (155)
30 1000Genomes NC_000001.10 - 193043016 Oct 11, 2018 (152)
31 gnomAD - Genomes NC_000001.11 - 193073886 Apr 25, 2021 (155)
32 KOREAN population from KRGDB NC_000001.10 - 193043016 Apr 25, 2020 (154)
33 Korean Genome Project NC_000001.11 - 193073886 Apr 25, 2020 (154)
34 Qatari NC_000001.10 - 193043016 Apr 25, 2020 (154)
35 SGDP_PRJ NC_000001.10 - 193043016 Apr 25, 2020 (154)
36 8.3KJPN NC_000001.10 - 193043016 Apr 25, 2021 (155)
37 TopMed NC_000001.11 - 193073886 Apr 25, 2021 (155)
38 ALFA NC_000001.11 - 193073886 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).

Associated ID History Updated (Build)
rs34475808 Oct 15, 2006 (127)
Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
34798841, 5781253875, ss3099104670 NC_000001.11:193073885:C:A NC_000001.11:193073885:C:A (self)
ss87916062, ss205506440, ss276153451, ss284199340, ss290691832 NC_000001.9:191309638:C:G NC_000001.11:193073885:C:G (self)
4824718, 3009642, 1241938, 2574495, 5654819, ss648589786, ss1293994286, ss1426060977, ss1919200008, ss2698132077, ss2764351809, ss2988180482, ss3343835073, ss3826560933, ss3850557515, ss3895832248, ss5147685512 NC_000001.10:193043015:C:G NC_000001.11:193073885:C:G (self)
2545429, 41379449, 5781253875, ss3099104671, ss3646850174, ss3688302637, ss3800138142, ss3946167428, ss4477773114 NC_000001.11:193073885:C:G NC_000001.11:193073885:C:G (self)
ss41084957 NT_004487.19:44531657:C:G NC_000001.11:193073885:C:G (self)
ss17324211, ss18069715, ss18243017 NT_004671.15:4398001:C:G NC_000001.11:193073885:C:G (self)
5781253875, ss3099104672 NC_000001.11:193073885:C:T NC_000001.11:193073885: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 rs10801171

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