Name: rs62149377
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.

rs62149377

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr2:60759441 (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: G>A / G>C
Variation Type: SNV Single Nucleotide Variation
Frequency: C=0.242427 (64168/264690, TOPMED)
C=0.14969 (4230/28258, 14KJPN)
C=0.14755 (2473/16760, 8.3KJPN) (+ 15 more)
C=0.18585 (2525/13586, ALFA)
C=0.1999 (1280/6404, 1000G_30x)
C=0.2033 (1018/5008, 1000G)
C=0.4143 (1856/4480, Estonian)
C=0.2639 (1017/3854, ALSPAC)
C=0.2659 (986/3708, TWINSUK)
C=0.1317 (386/2930, KOREAN)
C=0.1397 (256/1832, Korea1K)
C=0.248 (248/998, GoNL)
C=0.298 (179/600, NorthernSweden)
C=0.347 (75/216, Qatari)
C=0.048 (10/210, Vietnamese)
G=0.424 (78/184, SGDP_PRJ)
C=0.40 (16/40, GENOME_DK)
G=0.42 (11/26, Siberian)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: PAPOLG : 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: 20231103111315

Population	Group	Sample Size	Ref Allele	Alt Allele	Ref HMOZ	Alt HMOZ	HTRZ	HWEP
Total	Global	13586	G=0.81415	A=0.00000, C=0.18585	0.696747	0.068453	0.234801	32
European	Sub	10630	G=0.77046	A=0.00000, C=0.22954	0.625776	0.084854	0.28937	32
African	Sub	1846	G=0.9816	A=0.0000, C=0.0184	0.970748	0.007584	0.021668	32
African Others	Sub	62	G=1.00	A=0.00, C=0.00	1.0	0.0	0.0	N/A
African American	Sub	1784	G=0.9809	A=0.0000, C=0.0191	0.969731	0.007848	0.022422	32
Asian	Sub	100	G=1.00	A=0.00, C=0.00	1.0	0.0	0.0	N/A
East Asian	Sub	74	G=1.00	A=0.00, C=0.00	1.0	0.0	0.0	N/A
Other Asian	Sub	26	G=1.00	A=0.00, C=0.00	1.0	0.0	0.0	N/A
Latin American 1	Sub	90	G=1.00	A=0.00, C=0.00	1.0	0.0	0.0	N/A
Latin American 2	Sub	372	G=1.000	A=0.000, C=0.000	1.0	0.0	0.0	N/A
South Asian	Sub	64	G=1.00	A=0.00, C=0.00	1.0	0.0	0.0	N/A
Other	Sub	484	G=0.895	A=0.000, C=0.105	0.818182	0.028926	0.152893	5

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	G=0.757573	C=0.242427
14KJPN	JAPANESE	Study-wide	28258	G=0.85031	C=0.14969
8.3KJPN	JAPANESE	Study-wide	16760	G=0.85245	C=0.14755
Allele Frequency Aggregator	Total	Global	13586	G=0.81415	A=0.00000, C=0.18585
Allele Frequency Aggregator	European	Sub	10630	G=0.77046	A=0.00000, C=0.22954
Allele Frequency Aggregator	African	Sub	1846	G=0.9816	A=0.0000, C=0.0184
Allele Frequency Aggregator	Other	Sub	484	G=0.895	A=0.000, C=0.105
Allele Frequency Aggregator	Latin American 2	Sub	372	G=1.000	A=0.000, C=0.000
Allele Frequency Aggregator	Asian	Sub	100	G=1.00	A=0.00, C=0.00
Allele Frequency Aggregator	Latin American 1	Sub	90	G=1.00	A=0.00, C=0.00
Allele Frequency Aggregator	South Asian	Sub	64	G=1.00	A=0.00, C=0.00
1000Genomes_30x	Global	Study-wide	6404	G=0.8001	C=0.1999
1000Genomes_30x	African	Sub	1786	G=0.8108	C=0.1892
1000Genomes_30x	Europe	Sub	1266	G=0.6848	C=0.3152
1000Genomes_30x	South Asian	Sub	1202	G=0.8261	C=0.1739
1000Genomes_30x	East Asian	Sub	1170	G=0.9000	C=0.1000
1000Genomes_30x	American	Sub	980	G=0.779	C=0.221
1000Genomes	Global	Study-wide	5008	G=0.7967	C=0.2033
1000Genomes	African	Sub	1322	G=0.8033	C=0.1967
1000Genomes	East Asian	Sub	1008	G=0.8958	C=0.1042
1000Genomes	Europe	Sub	1006	G=0.6809	C=0.3191
1000Genomes	South Asian	Sub	978	G=0.826	C=0.174
1000Genomes	American	Sub	694	G=0.767	C=0.233
Genetic variation in the Estonian population	Estonian	Study-wide	4480	G=0.5857	C=0.4143
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	G=0.7361	C=0.2639
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	G=0.7341	C=0.2659
KOREAN population from KRGDB	KOREAN	Study-wide	2930	G=0.8683	C=0.1317
Korean Genome Project	KOREAN	Study-wide	1832	G=0.8603	C=0.1397
Genome of the Netherlands Release 5	Genome of the Netherlands	Study-wide	998	G=0.752	C=0.248
Northern Sweden	ACPOP	Study-wide	600	G=0.702	C=0.298
Qatari	Global	Study-wide	216	G=0.653	C=0.347
A Vietnamese Genetic Variation Database	Global	Study-wide	210	G=0.952	C=0.048
SGDP_PRJ	Global	Study-wide	184	G=0.424	C=0.576
The Danish reference pan genome	Danish	Study-wide	40	G=0.60	C=0.40
Siberian	Global	Study-wide	26	G=0.42	C=0.58

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 2	NC_000002.12:g.60759441G>A
GRCh38.p14 chr 2	NC_000002.12:g.60759441G>C
GRCh37.p13 chr 2	NC_000002.11:g.60986576G>A
GRCh37.p13 chr 2	NC_000002.11:g.60986576G>C

Gene: PAPOLG, poly(A) polymerase gamma (plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
PAPOLG transcript	NM_022894.4:c.18-693G>A	N/A	Intron Variant
PAPOLG transcript variant X1	XM_005264500.5:c.18-693G>A	N/A	Intron Variant
PAPOLG transcript variant X2	XM_005264501.3:c.-115-693… XM_005264501.3:c.-115-693G>A	N/A	Intron Variant
PAPOLG transcript variant X3	XR_007080681.1:n.	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	G=	A	C
GRCh38.p14 chr 2	NC_000002.12:g.60759441=	NC_000002.12:g.60759441G>A	NC_000002.12:g.60759441G>C
GRCh37.p13 chr 2	NC_000002.11:g.60986576=	NC_000002.11:g.60986576G>A	NC_000002.11:g.60986576G>C
PAPOLG transcript	NM_022894.3:c.18-693=	NM_022894.3:c.18-693G>A	NM_022894.3:c.18-693G>C
PAPOLG transcript	NM_022894.4:c.18-693=	NM_022894.4:c.18-693G>A	NM_022894.4:c.18-693G>C
PAPOLG transcript variant X1	XM_005264500.1:c.18-693=	XM_005264500.1:c.18-693G>A	XM_005264500.1:c.18-693G>C
PAPOLG transcript variant X1	XM_005264500.5:c.18-693=	XM_005264500.5:c.18-693G>A	XM_005264500.5:c.18-693G>C
PAPOLG transcript variant X2	XM_005264501.1:c.-115-693=	XM_005264501.1:c.-115-693G>A	XM_005264501.1:c.-115-693G>C
PAPOLG transcript variant X2	XM_005264501.3:c.-115-693=	XM_005264501.3:c.-115-693G>A	XM_005264501.3:c.-115-693G>C

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#.

64 SubSNP, 20 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	BCMHGSC_JDW	ss91183449	Mar 24, 2008 (129)
2	HUMANGENOME_JCVI	ss97043062	Feb 04, 2009 (130)
3	1000GENOMES	ss109568185	Jan 24, 2009 (130)
4	1000GENOMES	ss110359414	Jan 24, 2009 (130)
5	ENSEMBL	ss138454242	Dec 01, 2009 (131)
6	ENSEMBL	ss144163179	Dec 01, 2009 (131)
7	GMI	ss157133126	Dec 01, 2009 (131)
8	COMPLETE_GENOMICS	ss163505541	Jul 04, 2010 (132)
9	1000GENOMES	ss219282508	Jul 14, 2010 (132)
10	1000GENOMES	ss231194641	Jul 14, 2010 (132)
11	1000GENOMES	ss238743406	Jul 15, 2010 (132)
12	GMI	ss276493985	May 04, 2012 (137)
13	GMI	ss284356061	Apr 25, 2013 (138)
14	TISHKOFF	ss555606727	Apr 25, 2013 (138)
15	SSMP	ss649194178	Apr 25, 2013 (138)
16	EVA-GONL	ss976900395	Aug 21, 2014 (142)
17	JMKIDD_LAB	ss1069167928	Aug 21, 2014 (142)
18	1000GENOMES	ss1297487833	Aug 21, 2014 (142)
19	DDI	ss1428597173	Apr 01, 2015 (144)
20	EVA_GENOME_DK	ss1578906623	Apr 01, 2015 (144)
21	EVA_DECODE	ss1586314184	Apr 01, 2015 (144)
22	EVA_UK10K_ALSPAC	ss1603651591	Apr 01, 2015 (144)
23	EVA_UK10K_TWINSUK	ss1646645624	Apr 01, 2015 (144)
24	HAMMER_LAB	ss1796834344	Sep 08, 2015 (146)
25	WEILL_CORNELL_DGM	ss1920131765	Feb 12, 2016 (147)
26	GENOMED	ss1968786056	Jul 19, 2016 (147)
27	JJLAB	ss2020599992	Sep 14, 2016 (149)
28	ILLUMINA	ss2094902150	Dec 20, 2016 (150)
29	ILLUMINA	ss2095091923	Dec 20, 2016 (150)
30	USC_VALOUEV	ss2148643858	Dec 20, 2016 (150)
31	HUMAN_LONGEVITY	ss2230821216	Dec 20, 2016 (150)
32	SYSTEMSBIOZJU	ss2624810448	Nov 08, 2017 (151)
33	GRF	ss2703214394	Nov 08, 2017 (151)
34	GNOMAD	ss2774179646	Nov 08, 2017 (151)
35	AFFY	ss2985169849	Nov 08, 2017 (151)
36	SWEGEN	ss2989601426	Nov 08, 2017 (151)
37	BIOINF_KMB_FNS_UNIBA	ss3024066905	Nov 08, 2017 (151)
38	CSHL	ss3344257748	Nov 08, 2017 (151)
39	URBANLAB	ss3647045825	Oct 11, 2018 (152)
40	ILLUMINA	ss3652409171	Oct 11, 2018 (152)
41	EGCUT_WGS	ss3657577077	Jul 13, 2019 (153)
42	ACPOP	ss3728485931	Jul 13, 2019 (153)
43	EVA	ss3756835731	Jul 13, 2019 (153)
44	KHV_HUMAN_GENOMES	ss3801205719	Jul 13, 2019 (153)
45	EVA	ss3827011648	Apr 25, 2020 (154)
46	EVA	ss3836915811	Apr 25, 2020 (154)
47	EVA	ss3842331597	Apr 25, 2020 (154)
48	SGDP_PRJ	ss3852394924	Apr 25, 2020 (154)
49	KRGDB	ss3897875267	Apr 25, 2020 (154)
50	KOGIC	ss3947866845	Apr 25, 2020 (154)
51	TOPMED	ss4507909324	Apr 26, 2021 (155)
52	TOMMO_GENOMICS	ss5151634673	Apr 26, 2021 (155)
53	1000G_HIGH_COVERAGE	ss5248269394	Oct 12, 2022 (156)
54	EVA	ss5329320916	Oct 12, 2022 (156)
55	HUGCELL_USP	ss5448453619	Oct 12, 2022 (156)
56	EVA	ss5506430746	Oct 12, 2022 (156)
57	1000G_HIGH_COVERAGE	ss5523604171	Oct 12, 2022 (156)
58	SANFORD_IMAGENETICS	ss5628860618	Oct 12, 2022 (156)
59	TOMMO_GENOMICS	ss5680334020	Oct 12, 2022 (156)
60	YY_MCH	ss5802255628	Oct 12, 2022 (156)
61	EVA	ss5820178263	Oct 12, 2022 (156)
62	EVA	ss5852546073	Oct 12, 2022 (156)
63	EVA	ss5930610114	Oct 12, 2022 (156)
64	EVA	ss5955099387	Oct 12, 2022 (156)
65	1000Genomes	NC_000002.11 - 60986576	Oct 11, 2018 (152)
66	1000Genomes_30x	NC_000002.12 - 60759441	Oct 12, 2022 (156)
67	The Avon Longitudinal Study of Parents and Children	NC_000002.11 - 60986576	Oct 11, 2018 (152)
68	Genetic variation in the Estonian population	NC_000002.11 - 60986576	Oct 11, 2018 (152)
69	The Danish reference pan genome	NC_000002.11 - 60986576	Apr 25, 2020 (154)
70	gnomAD - Genomes Submission ignored due to conflicting rows: Row 59913721 (NC_000002.12:60759440:G:A 1/139988) Row 59913722 (NC_000002.12:60759440:G:C 36219/139918)	-	Apr 26, 2021 (155)
71	gnomAD - Genomes Submission ignored due to conflicting rows: Row 59913721 (NC_000002.12:60759440:G:A 1/139988) Row 59913722 (NC_000002.12:60759440:G:C 36219/139918)	-	Apr 26, 2021 (155)
72	Genome of the Netherlands Release 5	NC_000002.11 - 60986576	Apr 25, 2020 (154)
73	KOREAN population from KRGDB	NC_000002.11 - 60986576	Apr 25, 2020 (154)
74	Korean Genome Project	NC_000002.12 - 60759441	Apr 25, 2020 (154)
75	Northern Sweden	NC_000002.11 - 60986576	Jul 13, 2019 (153)
76	Qatari	NC_000002.11 - 60986576	Apr 25, 2020 (154)
77	SGDP_PRJ	NC_000002.11 - 60986576	Apr 25, 2020 (154)
78	Siberian	NC_000002.11 - 60986576	Apr 25, 2020 (154)
79	8.3KJPN	NC_000002.11 - 60986576	Apr 26, 2021 (155)
80	14KJPN	NC_000002.12 - 60759441	Oct 12, 2022 (156)
81	TopMed	NC_000002.12 - 60759441	Apr 26, 2021 (155)
82	UK 10K study - Twins	NC_000002.11 - 60986576	Oct 11, 2018 (152)
83	A Vietnamese Genetic Variation Database	NC_000002.11 - 60986576	Jul 13, 2019 (153)
84	ALFA	NC_000002.12 - 60759441	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).

Added to this RefSNP Cluster:

Submission IDs	Observation SPDI	Canonical SPDI	Source RSIDs
13292801289	NC_000002.12:60759440:G:A	NC_000002.12:60759440:G:A	(self)
ss91183449, ss109568185, ss110359414, ss163505541, ss276493985, ss284356061, ss1586314184, ss2094902150	NC_000002.10:60840079:G:C	NC_000002.12:60759440:G:C	(self)
8439836, 4693101, 3315325, 5077847, 2062895, 5052661, 1770796, 2173695, 4411904, 1160212, 9603980, 4693101, 1019853, ss219282508, ss231194641, ss238743406, ss555606727, ss649194178, ss976900395, ss1069167928, ss1297487833, ss1428597173, ss1578906623, ss1603651591, ss1646645624, ss1796834344, ss1920131765, ss1968786056, ss2020599992, ss2095091923, ss2148643858, ss2624810448, ss2703214394, ss2774179646, ss2985169849, ss2989601426, ss3344257748, ss3652409171, ss3657577077, ss3728485931, ss3756835731, ss3827011648, ss3836915811, ss3852394924, ss3897875267, ss5151634673, ss5329320916, ss5506430746, ss5628860618, ss5820178263, ss5955099387	NC_000002.11:60986575:G:C	NC_000002.12:60759440:G:C	(self)
11130106, 4244846, 14171124, 311732203, 13292801289, ss2230821216, ss3024066905, ss3647045825, ss3801205719, ss3842331597, ss3947866845, ss4507909324, ss5248269394, ss5448453619, ss5523604171, ss5680334020, ss5802255628, ss5852546073, ss5930610114	NC_000002.12:60759440:G:C	NC_000002.12:60759440:G:C	(self)
ss97043062, ss138454242, ss144163179, ss157133126	NT_022184.15:39808462:G:C	NC_000002.12:60759440:G: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 rs62149377

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

rs62149377