Name: rs10801171
Published: September 21, 2022
License: Open Access

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 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr1:193073886 (GRCh38.p14) 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=0.45194 (12724/28154, 14KJPN) (+ 7 more)
G=0.44131 (7369/16698, 8.3KJPN)
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

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: 20230706150541

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

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").

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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
14KJPN	JAPANESE	Study-wide	28154	C=0.54806	G=0.45194
8.3KJPN	JAPANESE	Study-wide	16698	C=0.55869	G=0.44131
Allele Frequency Aggregator	Total	Global	9730	C=0.8066	A=0.0000, G=0.1934, T=0.0000
Allele Frequency Aggregator	European	Sub	6816	C=0.7245	A=0.0000, G=0.2755, T=0.0000
Allele Frequency Aggregator	African	Sub	2374	C=1.0000	A=0.0000, G=0.0000, T=0.0000
Allele Frequency Aggregator	Other	Sub	208	C=0.981	A=0.000, G=0.019, T=0.000
Allele Frequency Aggregator	Latin American 2	Sub	206	C=1.000	A=0.000, G=0.000, T=0.000
Allele Frequency Aggregator	Latin American 1	Sub	68	C=1.00	A=0.00, G=0.00, T=0.00
Allele Frequency Aggregator	Asian	Sub	34	C=1.00	A=0.00, G=0.00, T=0.00
Allele Frequency Aggregator	South Asian	Sub	24	C=1.00	A=0.00, G=0.00, T=0.00
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

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.p14 chr 1	NC_000001.11:g.193073886C>A
GRCh38.p14 chr 1	NC_000001.11:g.193073886C>G
GRCh38.p14 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_006711495.5:c.647-1934… XM_006711495.5:c.647-1934C>A	N/A	Intron Variant
RO60 transcript variant X2	XM_006711496.4:c.647-1934… XM_006711496.4:c.647-1934C>A	N/A	Intron Variant
RO60 transcript variant X5	XM_006711497.4:c.581-1934… XM_006711497.4:c.581-1934C>A	N/A	Intron Variant
RO60 transcript variant X9	XM_011509922.3:c.-245-193… XM_011509922.3:c.-245-1934C>A	N/A	Intron Variant
RO60 transcript variant X4	XM_017002180.2:c.647-1934… XM_017002180.2:c.647-1934C>A	N/A	Intron Variant
RO60 transcript variant X6	XM_017002181.3:c.581-1934… XM_017002181.3:c.581-1934C>A	N/A	Intron Variant
RO60 transcript variant X7	XM_017002182.2:c.581-1934… XM_017002182.2:c.581-1934C>A	N/A	Intron Variant
RO60 transcript variant X10	XM_017002183.2:c.-24-2615… XM_017002183.2:c.-24-2615C>A	N/A	Intron Variant
RO60 transcript variant X3	XM_047428920.1:c.647-1934… XM_047428920.1:c.647-1934C>A	N/A	Intron Variant
RO60 transcript variant X8	XM_047428924.1:c.581-1934… XM_047428924.1:c.581-1934C>A	N/A	Intron Variant

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

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.p14 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_006711495.5:c.647-1934=	XM_006711495.5:c.647-1934C>A	XM_006711495.5:c.647-1934C>G	XM_006711495.5:c.647-1934C>T
RO60 transcript variant X2	XM_006711496.4:c.647-1934=	XM_006711496.4:c.647-1934C>A	XM_006711496.4:c.647-1934C>G	XM_006711496.4:c.647-1934C>T
RO60 transcript variant X5	XM_006711497.4:c.581-1934=	XM_006711497.4:c.581-1934C>A	XM_006711497.4:c.581-1934C>G	XM_006711497.4:c.581-1934C>T
RO60 transcript variant X9	XM_011509922.3:c.-245-1934=	XM_011509922.3:c.-245-1934C>A	XM_011509922.3:c.-245-1934C>G	XM_011509922.3:c.-245-1934C>T
RO60 transcript variant X4	XM_017002180.2:c.647-1934=	XM_017002180.2:c.647-1934C>A	XM_017002180.2:c.647-1934C>G	XM_017002180.2:c.647-1934C>T
RO60 transcript variant X6	XM_017002181.3:c.581-1934=	XM_017002181.3:c.581-1934C>A	XM_017002181.3:c.581-1934C>G	XM_017002181.3:c.581-1934C>T
RO60 transcript variant X7	XM_017002182.2:c.581-1934=	XM_017002182.2:c.581-1934C>A	XM_017002182.2:c.581-1934C>G	XM_017002182.2:c.581-1934C>T
RO60 transcript variant X10	XM_017002183.2:c.-24-2615=	XM_017002183.2:c.-24-2615C>A	XM_017002183.2:c.-24-2615C>G	XM_017002183.2:c.-24-2615C>T
RO60 transcript variant X3	XM_047428920.1:c.647-1934=	XM_047428920.1:c.647-1934C>A	XM_047428920.1:c.647-1934C>G	XM_047428920.1:c.647-1934C>T
RO60 transcript variant X8	XM_047428924.1:c.581-1934=	XM_047428924.1:c.581-1934C>A	XM_047428924.1:c.581-1934C>G	XM_047428924.1:c.581-1934C>T

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#.

32 SubSNP, 10 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	CSHL	ss3343835073	Nov 08, 2017 (151)
18	URBANLAB	ss3646850174	Oct 11, 2018 (152)
19	EVA_DECODE	ss3688302637	Jul 12, 2019 (153)
20	KHV_HUMAN_GENOMES	ss3800138142	Jul 12, 2019 (153)
21	EVA	ss3826560933	Apr 25, 2020 (154)
22	SGDP_PRJ	ss3850557515	Apr 25, 2020 (154)
23	KRGDB	ss3895832248	Apr 25, 2020 (154)
24	KOGIC	ss3946167428	Apr 25, 2020 (154)
25	TOPMED	ss4477773114	Apr 25, 2021 (155)
26	TOMMO_GENOMICS	ss5147685512	Apr 25, 2021 (155)
27	EVA	ss5323745805	Oct 12, 2022 (156)
28	EVA	ss5506129079	Oct 12, 2022 (156)
29	SANFORD_IMAGENETICS	ss5627120784	Oct 12, 2022 (156)
30	TOMMO_GENOMICS	ss5675228700	Oct 12, 2022 (156)
31	YY_MCH	ss5801493253	Oct 12, 2022 (156)
32	EVA	ss5833030733	Oct 12, 2022 (156)
33	1000Genomes	NC_000001.10 - 193043016	Oct 11, 2018 (152)
34	gnomAD - Genomes	NC_000001.11 - 193073886	Apr 25, 2021 (155)
35	KOREAN population from KRGDB	NC_000001.10 - 193043016	Apr 25, 2020 (154)
36	Korean Genome Project	NC_000001.11 - 193073886	Apr 25, 2020 (154)
37	Qatari	NC_000001.10 - 193043016	Apr 25, 2020 (154)
38	SGDP_PRJ	NC_000001.10 - 193043016	Apr 25, 2020 (154)
39	8.3KJPN	NC_000001.10 - 193043016	Apr 25, 2021 (155)
40	14KJPN	NC_000001.11 - 193073886	Oct 12, 2022 (156)
41	TopMed	NC_000001.11 - 193073886	Apr 25, 2021 (155)
42	ALFA	NC_000001.11 - 193073886	Apr 25, 2021 (155)

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	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, ss5323745805, ss5506129079, ss5627120784, ss5833030733	NC_000001.10:193043015:C:G	NC_000001.11:193073885:C:G	(self)
2545429, 9065804, 41379449, 5781253875, ss3646850174, ss3688302637, ss3800138142, ss3946167428, ss4477773114, ss5675228700, ss5801493253	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	NC_000001.11:193073885:C:T	NC_000001.11:193073885:C:T	(self)

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

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
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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.

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dbSNP Short Genetic Variations

Welcome to the Reference SNP (rs) Report

Reference SNP (rs) Report

rs10801171