Name: rs17342408
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.

rs17342408

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr1:31062047 (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: A>C
Variation Type: SNV Single Nucleotide Variation
Frequency: C=0.275794 (73000/264690, TOPMED)
C=0.287048 (40220/140116, GnomAD)
C=0.00032 (9/28258, 14KJPN) (+ 14 more)
C=0.31731 (5994/18890, ALFA)
C=0.00042 (7/16760, 8.3KJPN)
C=0.1994 (1277/6404, 1000G_30x)
C=0.1939 (971/5008, 1000G)
C=0.3672 (1645/4480, Estonian)
C=0.3415 (1316/3854, ALSPAC)
C=0.3522 (1306/3708, TWINSUK)
C=0.0010 (3/2922, KOREAN)
C=0.323 (322/998, GoNL)
C=0.378 (227/600, NorthernSweden)
C=0.213 (46/216, Qatari)
A=0.394 (74/188, SGDP_PRJ)
C=0.35 (14/40, GENOME_DK)
A=0.39 (7/18, Siberian)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: PUM1 : 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	18890	A=0.68269	C=0.31731
European	Sub	14286	A=0.65449	C=0.34551
African	Sub	2946	A=0.7980	C=0.2020
African Others	Sub	114	A=0.798	C=0.202
African American	Sub	2832	A=0.7980	C=0.2020
Asian	Sub	112	A=1.000	C=0.000
East Asian	Sub	86	A=1.00	C=0.00
Other Asian	Sub	26	A=1.00	C=0.00
Latin American 1	Sub	146	A=0.753	C=0.247
Latin American 2	Sub	610	A=0.666	C=0.334
South Asian	Sub	98	A=0.78	C=0.22
Other	Sub	692	A=0.710	C=0.290

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	A=0.724206	C=0.275794
gnomAD - Genomes	Global	Study-wide	140116	A=0.712952	C=0.287048
gnomAD - Genomes	European	Sub	75882	A=0.66087	C=0.33913
gnomAD - Genomes	African	Sub	41986	A=0.79095	C=0.20905
gnomAD - Genomes	American	Sub	13642	A=0.68678	C=0.31322
gnomAD - Genomes	Ashkenazi Jewish	Sub	3322	A=0.7471	C=0.2529
gnomAD - Genomes	East Asian	Sub	3132	A=0.9981	C=0.0019
gnomAD - Genomes	Other	Sub	2152	A=0.7258	C=0.2742
14KJPN	JAPANESE	Study-wide	28258	A=0.99968	C=0.00032
Allele Frequency Aggregator	Total	Global	18890	A=0.68269	C=0.31731
Allele Frequency Aggregator	European	Sub	14286	A=0.65449	C=0.34551
Allele Frequency Aggregator	African	Sub	2946	A=0.7980	C=0.2020
Allele Frequency Aggregator	Other	Sub	692	A=0.710	C=0.290
Allele Frequency Aggregator	Latin American 2	Sub	610	A=0.666	C=0.334
Allele Frequency Aggregator	Latin American 1	Sub	146	A=0.753	C=0.247
Allele Frequency Aggregator	Asian	Sub	112	A=1.000	C=0.000
Allele Frequency Aggregator	South Asian	Sub	98	A=0.78	C=0.22
8.3KJPN	JAPANESE	Study-wide	16760	A=0.99958	C=0.00042
1000Genomes_30x	Global	Study-wide	6404	A=0.8006	C=0.1994
1000Genomes_30x	African	Sub	1786	A=0.8287	C=0.1713
1000Genomes_30x	Europe	Sub	1266	A=0.7093	C=0.2907
1000Genomes_30x	South Asian	Sub	1202	A=0.7837	C=0.2163
1000Genomes_30x	East Asian	Sub	1170	A=0.9940	C=0.0060
1000Genomes_30x	American	Sub	980	A=0.657	C=0.343
1000Genomes	Global	Study-wide	5008	A=0.8061	C=0.1939
1000Genomes	African	Sub	1322	A=0.8230	C=0.1770
1000Genomes	East Asian	Sub	1008	A=0.9960	C=0.0040
1000Genomes	Europe	Sub	1006	A=0.7107	C=0.2893
1000Genomes	South Asian	Sub	978	A=0.780	C=0.220
1000Genomes	American	Sub	694	A=0.673	C=0.327
Genetic variation in the Estonian population	Estonian	Study-wide	4480	A=0.6328	C=0.3672
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	A=0.6585	C=0.3415
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	A=0.6478	C=0.3522
KOREAN population from KRGDB	KOREAN	Study-wide	2922	A=0.9990	C=0.0010
Genome of the Netherlands Release 5	Genome of the Netherlands	Study-wide	998	A=0.677	C=0.323
Northern Sweden	ACPOP	Study-wide	600	A=0.622	C=0.378
Qatari	Global	Study-wide	216	A=0.787	C=0.213
SGDP_PRJ	Global	Study-wide	188	A=0.394	C=0.606
The Danish reference pan genome	Danish	Study-wide	40	A=0.65	C=0.35
Siberian	Global	Study-wide	18	A=0.39	C=0.61

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.31062047A>C
GRCh37.p13 chr 1	NC_000001.10:g.31534894A>C

Gene: PUM1, pumilio RNA binding family member 1 (minus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
PUM1 transcript variant 1	NM_001020658.2:c.-11-2470… NM_001020658.2:c.-11-2470T>G	N/A	Intron Variant
PUM1 transcript variant 2	NM_014676.3:c.-11-2470T>G	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	A=	C
GRCh38.p14 chr 1	NC_000001.11:g.31062047=	NC_000001.11:g.31062047A>C
GRCh37.p13 chr 1	NC_000001.10:g.31534894=	NC_000001.10:g.31534894A>C
PUM1 transcript variant 1	NM_001020658.1:c.-11-2470=	NM_001020658.1:c.-11-2470T>G
PUM1 transcript variant 1	NM_001020658.2:c.-11-2470=	NM_001020658.2:c.-11-2470T>G
PUM1 transcript variant 2	NM_014676.2:c.-11-2470=	NM_014676.2:c.-11-2470T>G
PUM1 transcript variant 2	NM_014676.3:c.-11-2470=	NM_014676.3:c.-11-2470T>G
PUM1 transcript variant X1	XM_005271357.1:c.98-2470=	XM_005271357.1:c.98-2470T>G
PUM1 transcript variant X2	XM_005271358.1:c.98-2470=	XM_005271358.1:c.98-2470T>G
PUM1 transcript variant X3	XM_005271359.1:c.98-2470=	XM_005271359.1:c.98-2470T>G
PUM1 transcript variant X4	XM_005271360.1:c.-11-2470=	XM_005271360.1:c.-11-2470T>G
PUM1 transcript variant X5	XM_005271361.1:c.98-2470=	XM_005271361.1:c.98-2470T>G
PUM1 transcript variant X6	XM_005271362.1:c.-11-2470=	XM_005271362.1:c.-11-2470T>G
PUM1 transcript variant X7	XM_005271363.1:c.-11-2470=	XM_005271363.1:c.-11-2470T>G
PUM1 transcript variant X8	XM_005271364.1:c.-11-2470=	XM_005271364.1:c.-11-2470T>G

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#.

55 SubSNP, 17 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	PERLEGEN	ss24628660	Sep 20, 2004 (123)
2	HGSV	ss78164274	Dec 07, 2007 (129)
3	1000GENOMES	ss108098437	Jan 22, 2009 (130)
4	1000GENOMES	ss110252359	Jan 24, 2009 (130)
5	ILLUMINA-UK	ss118600771	Feb 14, 2009 (130)
6	COMPLETE_GENOMICS	ss163238426	Jul 04, 2010 (132)
7	COMPLETE_GENOMICS	ss166319883	Jul 04, 2010 (132)
8	BCM-HGSC-SUB	ss205197759	Jul 04, 2010 (132)
9	1000GENOMES	ss218309145	Jul 14, 2010 (132)
10	1000GENOMES	ss230480393	Jul 14, 2010 (132)
11	GMI	ss284027421	Apr 25, 2013 (138)
12	TISHKOFF	ss553947576	Apr 25, 2013 (138)
13	SSMP	ss647696768	Apr 25, 2013 (138)
14	EVA-GONL	ss975000182	Aug 21, 2014 (142)
15	JMKIDD_LAB	ss1067771405	Aug 21, 2014 (142)
16	1000GENOMES	ss1290248393	Aug 21, 2014 (142)
17	DDI	ss1425762346	Apr 01, 2015 (144)
18	EVA_GENOME_DK	ss1573970384	Apr 01, 2015 (144)
19	EVA_DECODE	ss1584359812	Apr 01, 2015 (144)
20	EVA_UK10K_ALSPAC	ss1599837322	Apr 01, 2015 (144)
21	EVA_UK10K_TWINSUK	ss1642831355	Apr 01, 2015 (144)
22	WEILL_CORNELL_DGM	ss1918212283	Feb 12, 2016 (147)
23	JJLAB	ss2019617650	Sep 14, 2016 (149)
24	USC_VALOUEV	ss2147626495	Dec 20, 2016 (150)
25	HUMAN_LONGEVITY	ss2161163320	Dec 20, 2016 (150)
26	GNOMAD	ss2753291059	Nov 08, 2017 (151)
27	SWEGEN	ss2986555037	Nov 08, 2017 (151)
28	BIOINF_KMB_FNS_UNIBA	ss3023574158	Nov 08, 2017 (151)
29	CSHL	ss3343389394	Nov 08, 2017 (151)
30	EGCUT_WGS	ss3654618274	Jul 12, 2019 (153)
31	EVA_DECODE	ss3686454198	Jul 12, 2019 (153)
32	ACPOP	ss3726912987	Jul 12, 2019 (153)
33	EVA	ss3746004797	Jul 12, 2019 (153)
34	PACBIO	ss3783368328	Jul 12, 2019 (153)
35	PACBIO	ss3789034784	Jul 12, 2019 (153)
36	PACBIO	ss3793907366	Jul 12, 2019 (153)
37	KHV_HUMAN_GENOMES	ss3799022926	Jul 12, 2019 (153)
38	EVA	ss3826097161	Apr 25, 2020 (154)
39	EVA	ss3836436594	Apr 25, 2020 (154)
40	EVA	ss3841841706	Apr 25, 2020 (154)
41	SGDP_PRJ	ss3848520848	Apr 25, 2020 (154)
42	KRGDB	ss3893460469	Apr 25, 2020 (154)
43	TOPMED	ss4444000168	Apr 25, 2021 (155)
44	TOMMO_GENOMICS	ss5143188922	Apr 25, 2021 (155)
45	1000G_HIGH_COVERAGE	ss5241702153	Oct 13, 2022 (156)
46	HUGCELL_USP	ss5442829443	Oct 13, 2022 (156)
47	EVA	ss5505803840	Oct 13, 2022 (156)
48	1000G_HIGH_COVERAGE	ss5513700589	Oct 13, 2022 (156)
49	SANFORD_IMAGENETICS	ss5625217056	Oct 13, 2022 (156)
50	TOMMO_GENOMICS	ss5667715939	Oct 13, 2022 (156)
51	YY_MCH	ss5800457455	Oct 13, 2022 (156)
52	EVA	ss5831743809	Oct 13, 2022 (156)
53	EVA	ss5848843325	Oct 13, 2022 (156)
54	EVA	ss5907611136	Oct 13, 2022 (156)
55	EVA	ss5937034457	Oct 13, 2022 (156)
56	1000Genomes	NC_000001.10 - 31534894	Oct 11, 2018 (152)
57	1000Genomes_30x	NC_000001.11 - 31062047	Oct 13, 2022 (156)
58	The Avon Longitudinal Study of Parents and Children	NC_000001.10 - 31534894	Oct 11, 2018 (152)
59	Genetic variation in the Estonian population	NC_000001.10 - 31534894	Oct 11, 2018 (152)
60	The Danish reference pan genome	NC_000001.10 - 31534894	Apr 25, 2020 (154)
61	gnomAD - Genomes	NC_000001.11 - 31062047	Apr 25, 2021 (155)
62	Genome of the Netherlands Release 5	NC_000001.10 - 31534894	Apr 25, 2020 (154)
63	KOREAN population from KRGDB	NC_000001.10 - 31534894	Apr 25, 2020 (154)
64	Northern Sweden	NC_000001.10 - 31534894	Jul 12, 2019 (153)
65	Qatari	NC_000001.10 - 31534894	Apr 25, 2020 (154)
66	SGDP_PRJ	NC_000001.10 - 31534894	Apr 25, 2020 (154)
67	Siberian	NC_000001.10 - 31534894	Apr 25, 2020 (154)
68	8.3KJPN	NC_000001.10 - 31534894	Apr 25, 2021 (155)
69	14KJPN	NC_000001.11 - 31062047	Oct 13, 2022 (156)
70	TopMed	NC_000001.11 - 31062047	Apr 25, 2021 (155)
71	UK 10K study - Twins	NC_000001.10 - 31534894	Oct 11, 2018 (152)
72	ALFA	NC_000001.11 - 31062047	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).

Added to this RefSNP Cluster:

Submission IDs	Observation SPDI	Canonical SPDI	Source RSIDs
ss78164274	NC_000001.8:31203986:A:C	NC_000001.11:31062046:A:C	(self)
ss108098437, ss110252359, ss118600771, ss163238426, ss166319883, ss205197759, ss284027421, ss1584359812	NC_000001.9:31307480:A:C	NC_000001.11:31062046:A:C	(self)
943872, 505631, 356522, 1444802, 217597, 637863, 197852, 254213, 537828, 142849, 1158229, 505631, ss218309145, ss230480393, ss553947576, ss647696768, ss975000182, ss1067771405, ss1290248393, ss1425762346, ss1573970384, ss1599837322, ss1642831355, ss1918212283, ss2019617650, ss2147626495, ss2753291059, ss2986555037, ss3343389394, ss3654618274, ss3726912987, ss3746004797, ss3783368328, ss3789034784, ss3793907366, ss3826097161, ss3836436594, ss3848520848, ss3893460469, ss5143188922, ss5505803840, ss5625217056, ss5831743809, ss5937034457	NC_000001.10:31534893:A:C	NC_000001.11:31062046:A:C	(self)
1226524, 6633439, 1553043, 7606503, 378746180, ss2161163320, ss3023574158, ss3686454198, ss3799022926, ss3841841706, ss4444000168, ss5241702153, ss5442829443, ss5513700589, ss5667715939, ss5800457455, ss5848843325, ss5907611136	NC_000001.11:31062046:A:C	NC_000001.11:31062046:A:C	(self)
ss24628660	NT_032977.9:1506811:A:C	NC_000001.11:31062046:A:C	(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 rs17342408

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.

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dbSNP Short Genetic Variations

Welcome to the Reference SNP (rs) Report

Reference SNP (rs) Report

rs17342408