Name: rs8179273
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.

rs8179273

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr1:99671072 (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>G
Variation Type: SNV Single Nucleotide Variation
Frequency: G=0.073104 (19350/264690, TOPMED)
G=0.067920 (9521/140180, GnomAD)
G=0.17596 (4972/28256, 14KJPN) (+ 18 more)
G=0.06019 (1137/18890, ALFA)
G=0.17792 (2982/16760, 8.3KJPN)
G=0.0982 (629/6404, 1000G_30x)
G=0.1018 (510/5008, 1000G)
G=0.0792 (355/4480, Estonian)
G=0.0410 (158/3854, ALSPAC)
G=0.0386 (143/3708, TWINSUK)
G=0.1925 (564/2930, KOREAN)
G=0.1932 (354/1832, Korea1K)
G=0.040 (40/998, GoNL)
G=0.053 (32/600, NorthernSweden)
G=0.081 (26/320, HapMap)
G=0.019 (4/216, Qatari)
G=0.131 (28/214, Vietnamese)
C=0.429 (60/140, SGDP_PRJ)
G=0.00 (0/50, Ancient Sardinia)
G=0.10 (4/40, GENOME_DK)
C=0.36 (10/28, Siberian)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: PALMD : 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	C=0.93981	G=0.06019
European	Sub	14286	C=0.94694	G=0.05306
African	Sub	2946	C=0.9437	G=0.0563
African Others	Sub	114	C=0.956	G=0.044
African American	Sub	2832	C=0.9431	G=0.0569
Asian	Sub	112	C=0.830	G=0.170
East Asian	Sub	86	C=0.83	G=0.17
Other Asian	Sub	26	C=0.85	G=0.15
Latin American 1	Sub	146	C=0.925	G=0.075
Latin American 2	Sub	610	C=0.785	G=0.215
South Asian	Sub	98	C=0.95	G=0.05
Other	Sub	692	C=0.932	G=0.068

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=0.926896	G=0.073104
gnomAD - Genomes	Global	Study-wide	140180	C=0.932080	G=0.067920
gnomAD - Genomes	European	Sub	75914	C=0.94649	G=0.05351
gnomAD - Genomes	African	Sub	42024	C=0.94065	G=0.05935
gnomAD - Genomes	American	Sub	13644	C=0.83539	G=0.16461
gnomAD - Genomes	Ashkenazi Jewish	Sub	3320	C=0.9777	G=0.0223
gnomAD - Genomes	East Asian	Sub	3128	C=0.8462	G=0.1538
gnomAD - Genomes	Other	Sub	2150	C=0.9237	G=0.0763
14KJPN	JAPANESE	Study-wide	28256	C=0.82404	G=0.17596
Allele Frequency Aggregator	Total	Global	18890	C=0.93981	G=0.06019
Allele Frequency Aggregator	European	Sub	14286	C=0.94694	G=0.05306
Allele Frequency Aggregator	African	Sub	2946	C=0.9437	G=0.0563
Allele Frequency Aggregator	Other	Sub	692	C=0.932	G=0.068
Allele Frequency Aggregator	Latin American 2	Sub	610	C=0.785	G=0.215
Allele Frequency Aggregator	Latin American 1	Sub	146	C=0.925	G=0.075
Allele Frequency Aggregator	Asian	Sub	112	C=0.830	G=0.170
Allele Frequency Aggregator	South Asian	Sub	98	C=0.95	G=0.05
8.3KJPN	JAPANESE	Study-wide	16760	C=0.82208	G=0.17792
1000Genomes_30x	Global	Study-wide	6404	C=0.9018	G=0.0982
1000Genomes_30x	African	Sub	1786	C=0.9323	G=0.0677
1000Genomes_30x	Europe	Sub	1266	C=0.9431	G=0.0569
1000Genomes_30x	South Asian	Sub	1202	C=0.9301	G=0.0699
1000Genomes_30x	East Asian	Sub	1170	C=0.8556	G=0.1444
1000Genomes_30x	American	Sub	980	C=0.813	G=0.187
1000Genomes	Global	Study-wide	5008	C=0.8982	G=0.1018
1000Genomes	African	Sub	1322	C=0.9312	G=0.0688
1000Genomes	East Asian	Sub	1008	C=0.8472	G=0.1528
1000Genomes	Europe	Sub	1006	C=0.9414	G=0.0586
1000Genomes	South Asian	Sub	978	C=0.928	G=0.072
1000Genomes	American	Sub	694	C=0.804	G=0.196
Genetic variation in the Estonian population	Estonian	Study-wide	4480	C=0.9208	G=0.0792
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	C=0.9590	G=0.0410
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	C=0.9614	G=0.0386
KOREAN population from KRGDB	KOREAN	Study-wide	2930	C=0.8075	G=0.1925
Korean Genome Project	KOREAN	Study-wide	1832	C=0.8068	G=0.1932
Genome of the Netherlands Release 5	Genome of the Netherlands	Study-wide	998	C=0.960	G=0.040
Northern Sweden	ACPOP	Study-wide	600	C=0.947	G=0.053
HapMap	Global	Study-wide	320	C=0.919	G=0.081
HapMap	African	Sub	118	C=0.932	G=0.068
HapMap	American	Sub	118	C=0.932	G=0.068
HapMap	Asian	Sub	84	C=0.88	G=0.12
Qatari	Global	Study-wide	216	C=0.981	G=0.019
A Vietnamese Genetic Variation Database	Global	Study-wide	214	C=0.869	G=0.131
SGDP_PRJ	Global	Study-wide	140	C=0.429	G=0.571
Ancient Sardinia genome-wide 1240k capture data generation and analysis	Global	Study-wide	50	C=1.00	G=0.00
The Danish reference pan genome	Danish	Study-wide	40	C=0.90	G=0.10
Siberian	Global	Study-wide	28	C=0.36	G=0.64

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.99671072C>G
GRCh37.p13 chr 1	NC_000001.10:g.100136628C>G

Gene: PALMD, palmdelphin (plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
PALMD transcript	NM_017734.5:c.251+3306C>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	C=	G
GRCh38.p14 chr 1	NC_000001.11:g.99671072=	NC_000001.11:g.99671072C>G
GRCh37.p13 chr 1	NC_000001.10:g.100136628=	NC_000001.10:g.100136628C>G
PALMD transcript	NM_017734.4:c.251+3306=	NM_017734.4:c.251+3306C>G
PALMD transcript	NM_017734.5:c.251+3306=	NM_017734.5:c.251+3306C>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#.

56 SubSNP, 21 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	SC_SNP	ss12568735	Aug 27, 2003 (117)
2	PERLEGEN	ss14883028	Dec 05, 2003 (119)
3	SC_SNP	ss15445264	Feb 27, 2004 (120)
4	PERLEGEN	ss23842724	Sep 20, 2004 (123)
5	AFFY	ss65921608	Dec 02, 2006 (127)
6	PERLEGEN	ss68775439	May 18, 2007 (127)
7	1000GENOMES	ss108454164	Jan 23, 2009 (130)
8	1000GENOMES	ss110891784	Jan 25, 2009 (130)
9	COMPLETE_GENOMICS	ss163740169	Jul 04, 2010 (132)
10	BCM-HGSC-SUB	ss205169111	Jul 04, 2010 (132)
11	1000GENOMES	ss218549025	Jul 14, 2010 (132)
12	1000GENOMES	ss230656970	Jul 14, 2010 (132)
13	1000GENOMES	ss238323880	Jul 15, 2010 (132)
14	GMI	ss275945506	May 04, 2012 (137)
15	SSMP	ss648254337	Apr 25, 2013 (138)
16	EVA-GONL	ss975483618	Aug 21, 2014 (142)
17	JMKIDD_LAB	ss1068128219	Aug 21, 2014 (142)
18	1000GENOMES	ss1292110190	Aug 21, 2014 (142)
19	EVA_GENOME_DK	ss1574271968	Apr 01, 2015 (144)
20	EVA_DECODE	ss1584861926	Apr 01, 2015 (144)
21	EVA_UK10K_ALSPAC	ss1600818317	Apr 01, 2015 (144)
22	EVA_UK10K_TWINSUK	ss1643812350	Apr 01, 2015 (144)
23	WEILL_CORNELL_DGM	ss1918683221	Feb 12, 2016 (147)
24	GENOMED	ss1966820900	Jul 19, 2016 (147)
25	JJLAB	ss2019863106	Sep 14, 2016 (149)
26	USC_VALOUEV	ss2147881776	Dec 20, 2016 (150)
27	HUMAN_LONGEVITY	ss2165036285	Dec 20, 2016 (150)
28	SYSTEMSBIOZJU	ss2624442969	Nov 08, 2017 (151)
29	GRF	ss2697809151	Nov 08, 2017 (151)
30	GNOMAD	ss2758644515	Nov 08, 2017 (151)
31	SWEGEN	ss2987306572	Nov 08, 2017 (151)
32	BIOINF_KMB_FNS_UNIBA	ss3023695153	Nov 08, 2017 (151)
33	CSHL	ss3343596185	Nov 08, 2017 (151)
34	EGCUT_WGS	ss3655391744	Jul 12, 2019 (153)
35	EVA_DECODE	ss3687368301	Jul 12, 2019 (153)
36	ACPOP	ss3727314574	Jul 12, 2019 (153)
37	EVA	ss3746574841	Jul 12, 2019 (153)
38	KHV_HUMAN_GENOMES	ss3799575615	Jul 12, 2019 (153)
39	SGDP_PRJ	ss3849478794	Apr 25, 2020 (154)
40	KRGDB	ss3894556862	Apr 25, 2020 (154)
41	KOGIC	ss3945092351	Apr 25, 2020 (154)
42	EVA	ss3984815022	Apr 25, 2021 (155)
43	TOPMED	ss4460719306	Apr 25, 2021 (155)
44	TOMMO_GENOMICS	ss5145315792	Apr 25, 2021 (155)
45	1000G_HIGH_COVERAGE	ss5243323846	Oct 12, 2022 (156)
46	EVA	ss5320677598	Oct 12, 2022 (156)
47	HUGCELL_USP	ss5444276085	Oct 12, 2022 (156)
48	EVA	ss5505964461	Oct 12, 2022 (156)
49	1000G_HIGH_COVERAGE	ss5516167765	Oct 12, 2022 (156)
50	SANFORD_IMAGENETICS	ss5626133096	Oct 12, 2022 (156)
51	TOMMO_GENOMICS	ss5670476067	Oct 12, 2022 (156)
52	YY_MCH	ss5800860311	Oct 12, 2022 (156)
53	EVA	ss5832372925	Oct 12, 2022 (156)
54	EVA	ss5849033926	Oct 12, 2022 (156)
55	EVA	ss5909476126	Oct 12, 2022 (156)
56	EVA	ss5937994206	Oct 12, 2022 (156)
57	1000Genomes	NC_000001.10 - 100136628	Oct 11, 2018 (152)
58	1000Genomes_30x	NC_000001.11 - 99671072	Oct 12, 2022 (156)
59	The Avon Longitudinal Study of Parents and Children	NC_000001.10 - 100136628	Oct 11, 2018 (152)
60	Genetic variation in the Estonian population	NC_000001.10 - 100136628	Oct 11, 2018 (152)
61	The Danish reference pan genome	NC_000001.10 - 100136628	Apr 25, 2020 (154)
62	gnomAD - Genomes	NC_000001.11 - 99671072	Apr 25, 2021 (155)
63	Genome of the Netherlands Release 5	NC_000001.10 - 100136628	Apr 25, 2020 (154)
64	HapMap	NC_000001.11 - 99671072	Apr 25, 2020 (154)
65	KOREAN population from KRGDB	NC_000001.10 - 100136628	Apr 25, 2020 (154)
66	Korean Genome Project	NC_000001.11 - 99671072	Apr 25, 2020 (154)
67	Northern Sweden	NC_000001.10 - 100136628	Jul 12, 2019 (153)
68	Ancient Sardinia genome-wide 1240k capture data generation and analysis	NC_000001.10 - 100136628	Apr 25, 2021 (155)
69	Qatari	NC_000001.10 - 100136628	Apr 25, 2020 (154)
70	SGDP_PRJ	NC_000001.10 - 100136628	Apr 25, 2020 (154)
71	Siberian	NC_000001.10 - 100136628	Apr 25, 2020 (154)
72	8.3KJPN	NC_000001.10 - 100136628	Apr 25, 2021 (155)
73	14KJPN	NC_000001.11 - 99671072	Oct 12, 2022 (156)
74	TopMed	NC_000001.11 - 99671072	Apr 25, 2021 (155)
75	UK 10K study - Twins	NC_000001.10 - 100136628	Oct 11, 2018 (152)
76	A Vietnamese Genetic Variation Database	NC_000001.10 - 100136628	Jul 12, 2019 (153)
77	ALFA	NC_000001.11 - 99671072	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)
rs17120878	Oct 07, 2004 (123)

Added to this RefSNP Cluster:

Submission IDs	Observation SPDI	Canonical SPDI	Source RSIDs
ss108454164, ss110891784, ss163740169, ss205169111, ss275945506, ss1584861926	NC_000001.9:99909215:C:G	NC_000001.11:99671071:C:G	(self)
2873837, 1585354, 1129992, 1629186, 687711, 1734256, 599439, 40949, 725151, 1495774, 398130, 3285099, 1585354, 341487, ss218549025, ss230656970, ss238323880, ss648254337, ss975483618, ss1068128219, ss1292110190, ss1574271968, ss1600818317, ss1643812350, ss1918683221, ss1966820900, ss2019863106, ss2147881776, ss2624442969, ss2697809151, ss2758644515, ss2987306572, ss3343596185, ss3655391744, ss3727314574, ss3746574841, ss3849478794, ss3894556862, ss3984815022, ss5145315792, ss5320677598, ss5505964461, ss5626133096, ss5832372925, ss5937994206	NC_000001.10:100136627:C:G	NC_000001.11:99671071:C:G	(self)
3693700, 20314241, 136753, 1470352, 4313171, 24325641, 328056127, ss2165036285, ss3023695153, ss3687368301, ss3799575615, ss3945092351, ss4460719306, ss5243323846, ss5444276085, ss5516167765, ss5670476067, ss5800860311, ss5849033926, ss5909476126	NC_000001.11:99671071:C:G	NC_000001.11:99671071:C:G	(self)
ss12568735, ss14883028, ss15445264, ss23842724, ss65921608, ss68775439	NT_032977.9:70108545:C:G	NC_000001.11:99671071:C:G	(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 rs8179273

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

rs8179273