Name: rs17548252
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.

rs17548252

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr6:3098696 (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>T
Variation Type: SNV Single Nucleotide Variation
Frequency: T=0.015184 (4019/264690, TOPMED)
T=0.020736 (2908/140242, GnomAD)
T=0.02615 (915/34994, ALFA) (+ 13 more)
T=0.00004 (1/28258, 14KJPN)
T=0.00006 (1/16760, 8.3KJPN)
T=0.0077 (49/6404, 1000G_30x)
T=0.0078 (39/5008, 1000G)
T=0.0540 (242/4480, Estonian)
T=0.0296 (114/3854, ALSPAC)
T=0.0297 (110/3708, TWINSUK)
T=0.0035 (4/1136, Daghestan)
T=0.019 (19/998, GoNL)
T=0.023 (14/600, NorthernSweden)
T=0.07 (3/40, GENOME_DK)
C=0.5 (2/4, SGDP_PRJ)
T=0.5 (2/4, SGDP_PRJ)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: RIPK1 : 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	34994	C=0.97385	T=0.02615
European	Sub	27636	C=0.96950	T=0.03050
African	Sub	4286	C=0.9960	T=0.0040
African Others	Sub	154	C=1.000	T=0.000
African American	Sub	4132	C=0.9959	T=0.0041
Asian	Sub	130	C=1.000	T=0.000
East Asian	Sub	102	C=1.000	T=0.000
Other Asian	Sub	28	C=1.00	T=0.00
Latin American 1	Sub	168	C=0.988	T=0.012
Latin American 2	Sub	700	C=0.984	T=0.016
South Asian	Sub	116	C=1.000	T=0.000
Other	Sub	1958	C=0.9785	T=0.0215

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=0.984816	T=0.015184
gnomAD - Genomes	Global	Study-wide	140242	C=0.979264	T=0.020736
gnomAD - Genomes	European	Sub	75934	C=0.96795	T=0.03205
gnomAD - Genomes	African	Sub	42040	C=0.99610	T=0.00390
gnomAD - Genomes	American	Sub	13658	C=0.98477	T=0.01523
gnomAD - Genomes	Ashkenazi Jewish	Sub	3324	C=0.9795	T=0.0205
gnomAD - Genomes	East Asian	Sub	3134	C=1.0000	T=0.0000
gnomAD - Genomes	Other	Sub	2152	C=0.9842	T=0.0158
Allele Frequency Aggregator	Total	Global	34994	C=0.97385	T=0.02615
Allele Frequency Aggregator	European	Sub	27636	C=0.96950	T=0.03050
Allele Frequency Aggregator	African	Sub	4286	C=0.9960	T=0.0040
Allele Frequency Aggregator	Other	Sub	1958	C=0.9785	T=0.0215
Allele Frequency Aggregator	Latin American 2	Sub	700	C=0.984	T=0.016
Allele Frequency Aggregator	Latin American 1	Sub	168	C=0.988	T=0.012
Allele Frequency Aggregator	Asian	Sub	130	C=1.000	T=0.000
Allele Frequency Aggregator	South Asian	Sub	116	C=1.000	T=0.000
14KJPN	JAPANESE	Study-wide	28258	C=0.99996	T=0.00004
8.3KJPN	JAPANESE	Study-wide	16760	C=0.99994	T=0.00006
1000Genomes_30x	Global	Study-wide	6404	C=0.9923	T=0.0077
1000Genomes_30x	African	Sub	1786	C=0.9994	T=0.0006
1000Genomes_30x	Europe	Sub	1266	C=0.9739	T=0.0261
1000Genomes_30x	South Asian	Sub	1202	C=0.9967	T=0.0033
1000Genomes_30x	East Asian	Sub	1170	C=1.0000	T=0.0000
1000Genomes_30x	American	Sub	980	C=0.989	T=0.011
1000Genomes	Global	Study-wide	5008	C=0.9922	T=0.0078
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=0.9742	T=0.0258
1000Genomes	South Asian	Sub	978	C=0.996	T=0.004
1000Genomes	American	Sub	694	C=0.988	T=0.012
Genetic variation in the Estonian population	Estonian	Study-wide	4480	C=0.9460	T=0.0540
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	C=0.9704	T=0.0296
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	C=0.9703	T=0.0297
Genome-wide autozygosity in Daghestan	Global	Study-wide	1136	C=0.9965	T=0.0035
Genome-wide autozygosity in Daghestan	Daghestan	Sub	628	C=0.997	T=0.003
Genome-wide autozygosity in Daghestan	Near_East	Sub	144	C=1.000	T=0.000
Genome-wide autozygosity in Daghestan	Central Asia	Sub	122	C=1.000	T=0.000
Genome-wide autozygosity in Daghestan	Europe	Sub	108	C=0.981	T=0.019
Genome-wide autozygosity in Daghestan	South Asian	Sub	98	C=1.00	T=0.00
Genome-wide autozygosity in Daghestan	Caucasus	Sub	36	C=1.00	T=0.00
Genome of the Netherlands Release 5	Genome of the Netherlands	Study-wide	998	C=0.981	T=0.019
Northern Sweden	ACPOP	Study-wide	600	C=0.977	T=0.023
The Danish reference pan genome	Danish	Study-wide	40	C=0.93	T=0.07
SGDP_PRJ	Global	Study-wide	4	C=0.5	T=0.5

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 6	NC_000006.12:g.3098696C>T
GRCh37.p13 chr 6	NC_000006.11:g.3098930C>T
RIPK1 RefSeqGene	NG_063914.1:g.39856C>T

Gene: RIPK1, receptor interacting serine/threonine kinase 1 (plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
RIPK1 transcript variant 2	NM_001317061.3:c.427-5529… NM_001317061.3:c.427-5529C>T	N/A	Intron Variant
RIPK1 transcript variant 3	NM_001354930.2:c.916-5529… NM_001354930.2:c.916-5529C>T	N/A	Intron Variant
RIPK1 transcript variant 4	NM_001354931.2:c.778-5529… NM_001354931.2:c.778-5529C>T	N/A	Intron Variant
RIPK1 transcript variant 5	NM_001354932.2:c.427-5529… NM_001354932.2:c.427-5529C>T	N/A	Intron Variant
RIPK1 transcript variant 6	NM_001354933.2:c.427-5529… NM_001354933.2:c.427-5529C>T	N/A	Intron Variant
RIPK1 transcript variant 7	NM_001354934.2:c.427-5529… NM_001354934.2:c.427-5529C>T	N/A	Intron Variant
RIPK1 transcript variant 1	NM_003804.6:c.916-5529C>T	N/A	Intron Variant
RIPK1 transcript variant X3	XM_017011403.2:c.427-5529… XM_017011403.2:c.427-5529C>T	N/A	Intron Variant
RIPK1 transcript variant X4	XM_017011404.3:c.48+4308C… XM_017011404.3:c.48+4308C>T	N/A	Intron Variant
RIPK1 transcript variant X6	XM_047419445.1:c.1039-552… XM_047419445.1:c.1039-5529C>T	N/A	Intron Variant
RIPK1 transcript variant X7	XM_047419446.1:c.1039-552… XM_047419446.1:c.1039-5529C>T	N/A	Intron Variant
RIPK1 transcript variant X8	XM_047419447.1:c.916-5529… XM_047419447.1:c.916-5529C>T	N/A	Intron Variant
RIPK1 transcript variant X1	XM_047419448.1:c.916-5529… XM_047419448.1:c.916-5529C>T	N/A	Intron Variant
RIPK1 transcript variant X2	XM_006715237.4:c.	N/A	Genic Downstream Transcript Variant
RIPK1 transcript variant X5	XM_017011405.2:c.	N/A	Genic Downstream Transcript 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=	T
GRCh38.p14 chr 6	NC_000006.12:g.3098696=	NC_000006.12:g.3098696C>T
GRCh37.p13 chr 6	NC_000006.11:g.3098930=	NC_000006.11:g.3098930C>T
RIPK1 RefSeqGene	NG_063914.1:g.39856=	NG_063914.1:g.39856C>T
RIPK1 transcript variant 2	NM_001317061.3:c.427-5529=	NM_001317061.3:c.427-5529C>T
RIPK1 transcript variant 3	NM_001354930.2:c.916-5529=	NM_001354930.2:c.916-5529C>T
RIPK1 transcript variant 4	NM_001354931.2:c.778-5529=	NM_001354931.2:c.778-5529C>T
RIPK1 transcript variant 5	NM_001354932.2:c.427-5529=	NM_001354932.2:c.427-5529C>T
RIPK1 transcript variant 6	NM_001354933.2:c.427-5529=	NM_001354933.2:c.427-5529C>T
RIPK1 transcript variant 7	NM_001354934.2:c.427-5529=	NM_001354934.2:c.427-5529C>T
RIPK1 transcript	NM_003804.3:c.916-5529=	NM_003804.3:c.916-5529C>T
RIPK1 transcript variant 1	NM_003804.6:c.916-5529=	NM_003804.6:c.916-5529C>T
RIPK1 transcript variant X1	XM_005249457.1:c.1426-5529=	XM_005249457.1:c.1426-5529C>T
RIPK1 transcript variant X3	XM_005249458.1:c.916-5529=	XM_005249458.1:c.916-5529C>T
RIPK1 transcript variant X3	XM_017011403.2:c.427-5529=	XM_017011403.2:c.427-5529C>T
RIPK1 transcript variant X4	XM_017011404.3:c.48+4308=	XM_017011404.3:c.48+4308C>T
RIPK1 transcript variant X6	XM_047419445.1:c.1039-5529=	XM_047419445.1:c.1039-5529C>T
RIPK1 transcript variant X7	XM_047419446.1:c.1039-5529=	XM_047419446.1:c.1039-5529C>T
RIPK1 transcript variant X8	XM_047419447.1:c.916-5529=	XM_047419447.1:c.916-5529C>T
RIPK1 transcript variant X1	XM_047419448.1:c.916-5529=	XM_047419448.1:c.916-5529C>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#.

43 SubSNP, 15 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	PGA-UW-FHCRC	ss28475999	Sep 20, 2004 (123)
2	ILLUMINA	ss172848282	Jul 04, 2010 (132)
3	1000GENOMES	ss233296916	Jul 14, 2010 (132)
4	ILLUMINA	ss244283887	Jul 04, 2010 (132)
5	ILLUMINA	ss483500547	May 04, 2012 (137)
6	ILLUMINA	ss485225961	May 04, 2012 (137)
7	ILLUMINA	ss535708696	Sep 08, 2015 (146)
8	ILLUMINA	ss779508823	Sep 08, 2015 (146)
9	ILLUMINA	ss782193694	Sep 08, 2015 (146)
10	ILLUMINA	ss834979151	Sep 08, 2015 (146)
11	EVA-GONL	ss982517360	Aug 21, 2014 (142)
12	1000GENOMES	ss1318722696	Aug 21, 2014 (142)
13	HAMMER_LAB	ss1397438744	Sep 08, 2015 (146)
14	EVA_GENOME_DK	ss1581505007	Apr 01, 2015 (144)
15	EVA_DECODE	ss1592062980	Apr 01, 2015 (144)
16	EVA_UK10K_ALSPAC	ss1614813692	Apr 01, 2015 (144)
17	EVA_UK10K_TWINSUK	ss1657807725	Apr 01, 2015 (144)
18	JJLAB	ss2023501913	Sep 14, 2016 (149)
19	HUMAN_LONGEVITY	ss2281280444	Dec 20, 2016 (150)
20	ILLUMINA	ss2634390699	Nov 08, 2017 (151)
21	ILLUMINA	ss2635153077	Nov 08, 2017 (151)
22	GNOMAD	ss2835100340	Nov 08, 2017 (151)
23	SWEGEN	ss2998414212	Nov 08, 2017 (151)
24	ILLUMINA	ss3629428444	Oct 12, 2018 (152)
25	ILLUMINA	ss3632311326	Oct 12, 2018 (152)
26	ILLUMINA	ss3638603083	Oct 12, 2018 (152)
27	EGCUT_WGS	ss3666337282	Jul 13, 2019 (153)
28	EVA_DECODE	ss3716457395	Jul 13, 2019 (153)
29	ACPOP	ss3733146695	Jul 13, 2019 (153)
30	KHV_HUMAN_GENOMES	ss3807694675	Jul 13, 2019 (153)
31	SGDP_PRJ	ss3863785783	Apr 26, 2020 (154)
32	EVA	ss4017251502	Apr 26, 2021 (155)
33	TOPMED	ss4691609949	Apr 26, 2021 (155)
34	TOMMO_GENOMICS	ss5175879879	Apr 26, 2021 (155)
35	1000G_HIGH_COVERAGE	ss5267180266	Oct 13, 2022 (156)
36	EVA	ss5363409683	Oct 13, 2022 (156)
37	HUGCELL_USP	ss5464994435	Oct 13, 2022 (156)
38	1000G_HIGH_COVERAGE	ss5552503054	Oct 13, 2022 (156)
39	SANFORD_IMAGENETICS	ss5639640479	Oct 13, 2022 (156)
40	TOMMO_GENOMICS	ss5713465336	Oct 13, 2022 (156)
41	EVA	ss5841705549	Oct 13, 2022 (156)
42	EVA	ss5882400415	Oct 13, 2022 (156)
43	EVA	ss5968133349	Oct 13, 2022 (156)
44	1000Genomes	NC_000006.11 - 3098930	Oct 12, 2018 (152)
45	1000Genomes_30x	NC_000006.12 - 3098696	Oct 13, 2022 (156)
46	The Avon Longitudinal Study of Parents and Children	NC_000006.11 - 3098930	Oct 12, 2018 (152)
47	Genome-wide autozygosity in Daghestan	NC_000006.10 - 3043929	Apr 26, 2020 (154)
48	Genetic variation in the Estonian population	NC_000006.11 - 3098930	Oct 12, 2018 (152)
49	The Danish reference pan genome	NC_000006.11 - 3098930	Apr 26, 2020 (154)
50	gnomAD - Genomes	NC_000006.12 - 3098696	Apr 26, 2021 (155)
51	Genome of the Netherlands Release 5	NC_000006.11 - 3098930	Apr 26, 2020 (154)
52	Northern Sweden	NC_000006.11 - 3098930	Jul 13, 2019 (153)
53	SGDP_PRJ	NC_000006.11 - 3098930	Apr 26, 2020 (154)
54	8.3KJPN	NC_000006.11 - 3098930	Apr 26, 2021 (155)
55	14KJPN	NC_000006.12 - 3098696	Oct 13, 2022 (156)
56	TopMed	NC_000006.12 - 3098696	Apr 26, 2021 (155)
57	UK 10K study - Twins	NC_000006.11 - 3098930	Oct 12, 2018 (152)
58	ALFA	NC_000006.12 - 3098696	Apr 26, 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)
rs386486663	Aug 21, 2014 (142)

Added to this RefSNP Cluster:

Submission IDs	Observation SPDI	Canonical SPDI	Source RSIDs
413484, ss485225961, ss1397438744, ss1592062980, ss2635153077	NC_000006.10:3043928:C:T	NC_000006.12:3098695:C:T	(self)
30455311, 16951160, 12075530, 7669946, 7524185, 6431560, 15802763, 33849186, 16951160, ss233296916, ss483500547, ss535708696, ss779508823, ss782193694, ss834979151, ss982517360, ss1318722696, ss1581505007, ss1614813692, ss1657807725, ss2023501913, ss2634390699, ss2835100340, ss2998414212, ss3629428444, ss3632311326, ss3638603083, ss3666337282, ss3733146695, ss3863785783, ss4017251502, ss5175879879, ss5363409683, ss5639640479, ss5841705549, ss5968133349	NC_000006.11:3098929:C:T	NC_000006.12:3098695:C:T	(self)
40028989, 215350620, 47302440, 528987507, 8248846245, ss2281280444, ss3716457395, ss3807694675, ss4691609949, ss5267180266, ss5464994435, ss5552503054, ss5713465336, ss5882400415	NC_000006.12:3098695:C:T	NC_000006.12:3098695:C:T	(self)
ss28475999, ss172848282, ss244283887	NT_007592.15:3038929:C:T	NC_000006.12:3098695: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 rs17548252

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

rs17548252