Name: rs7546846
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.

rs7546846

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr1:205836617 (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 / C>T
Variation Type: SNV Single Nucleotide Variation
Frequency: T=0.132087 (34962/264690, TOPMED)
T=0.114310 (16015/140102, GnomAD)
T=0.31806 (8987/28256, 14KJPN) (+ 16 more)
T=0.31641 (5303/16760, 8.3KJPN)
T=0.03868 (633/16366, ALFA)
T=0.1775 (1137/6404, 1000G_30x)
T=0.1821 (912/5008, 1000G)
T=0.0746 (334/4480, Estonian)
T=0.1131 (436/3854, ALSPAC)
T=0.1092 (405/3708, TWINSUK)
T=0.2840 (832/2930, KOREAN)
T=0.111 (111/998, GoNL)
T=0.105 (63/600, NorthernSweden)
T=0.097 (21/216, Qatari)
T=0.308 (66/214, Vietnamese)
C=0.418 (82/196, SGDP_PRJ)
T=0.10 (4/40, GENOME_DK)
C=0.50 (6/12, Siberian)
T=0.50 (6/12, Siberian)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: PM20D1 : 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	16366	C=0.96132	G=0.00000, T=0.03868
European	Sub	12724	C=0.95269	G=0.00000, T=0.04731
African	Sub	2556	C=0.9965	G=0.0000, T=0.0035
African Others	Sub	96	C=1.00	G=0.00, T=0.00
African American	Sub	2460	C=0.9963	G=0.0000, T=0.0037
Asian	Sub	60	C=1.00	G=0.00, T=0.00
East Asian	Sub	44	C=1.00	G=0.00, T=0.00
Other Asian	Sub	16	C=1.00	G=0.00, T=0.00
Latin American 1	Sub	114	C=1.000	G=0.000, T=0.000
Latin American 2	Sub	272	C=1.000	G=0.000, T=0.000
South Asian	Sub	60	C=0.98	G=0.00, T=0.02
Other	Sub	580	C=0.964	G=0.000, T=0.036

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=0.867913	T=0.132087
gnomAD - Genomes	Global	Study-wide	140102	C=0.885690	T=0.114310
gnomAD - Genomes	European	Sub	75876	C=0.89348	T=0.10652
gnomAD - Genomes	African	Sub	41992	C=0.92029	T=0.07971
gnomAD - Genomes	American	Sub	13636	C=0.77024	T=0.22976
gnomAD - Genomes	Ashkenazi Jewish	Sub	3324	C=0.9299	T=0.0701
gnomAD - Genomes	East Asian	Sub	3124	C=0.7045	T=0.2955
gnomAD - Genomes	Other	Sub	2150	C=0.8619	T=0.1381
14KJPN	JAPANESE	Study-wide	28256	C=0.68194	T=0.31806
8.3KJPN	JAPANESE	Study-wide	16760	C=0.68359	T=0.31641
Allele Frequency Aggregator	Total	Global	16366	C=0.96132	G=0.00000, T=0.03868
Allele Frequency Aggregator	European	Sub	12724	C=0.95269	G=0.00000, T=0.04731
Allele Frequency Aggregator	African	Sub	2556	C=0.9965	G=0.0000, T=0.0035
Allele Frequency Aggregator	Other	Sub	580	C=0.964	G=0.000, T=0.036
Allele Frequency Aggregator	Latin American 2	Sub	272	C=1.000	G=0.000, T=0.000
Allele Frequency Aggregator	Latin American 1	Sub	114	C=1.000	G=0.000, T=0.000
Allele Frequency Aggregator	South Asian	Sub	60	C=0.98	G=0.00, T=0.02
Allele Frequency Aggregator	Asian	Sub	60	C=1.00	G=0.00, T=0.00
1000Genomes_30x	Global	Study-wide	6404	C=0.8225	T=0.1775
1000Genomes_30x	African	Sub	1786	C=0.9250	T=0.0750
1000Genomes_30x	Europe	Sub	1266	C=0.8949	T=0.1051
1000Genomes_30x	South Asian	Sub	1202	C=0.8344	T=0.1656
1000Genomes_30x	East Asian	Sub	1170	C=0.6786	T=0.3214
1000Genomes_30x	American	Sub	980	C=0.699	T=0.301
1000Genomes	Global	Study-wide	5008	C=0.8179	T=0.1821
1000Genomes	African	Sub	1322	C=0.9221	T=0.0779
1000Genomes	East Asian	Sub	1008	C=0.6756	T=0.3244
1000Genomes	Europe	Sub	1006	C=0.8907	T=0.1093
1000Genomes	South Asian	Sub	978	C=0.839	T=0.161
1000Genomes	American	Sub	694	C=0.690	T=0.310
Genetic variation in the Estonian population	Estonian	Study-wide	4480	C=0.9254	T=0.0746
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	C=0.8869	T=0.1131
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	C=0.8908	T=0.1092
KOREAN population from KRGDB	KOREAN	Study-wide	2930	C=0.7160	T=0.2840
Genome of the Netherlands Release 5	Genome of the Netherlands	Study-wide	998	C=0.889	T=0.111
Northern Sweden	ACPOP	Study-wide	600	C=0.895	T=0.105
Qatari	Global	Study-wide	216	C=0.903	T=0.097
A Vietnamese Genetic Variation Database	Global	Study-wide	214	C=0.692	T=0.308
SGDP_PRJ	Global	Study-wide	196	C=0.418	T=0.582
The Danish reference pan genome	Danish	Study-wide	40	C=0.90	T=0.10
Siberian	Global	Study-wide	12	C=0.50	T=0.50

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.205836617C>G
GRCh38.p14 chr 1	NC_000001.11:g.205836617C>T
GRCh37.p13 chr 1	NC_000001.10:g.205805745C>G
GRCh37.p13 chr 1	NC_000001.10:g.205805745C>T

Gene: PM20D1, peptidase M20 domain containing 1 (minus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
PM20D1 transcript variant 1	NM_152491.5:c.1116+3635G>C	N/A	Intron Variant
PM20D1 transcript variant 2	NR_135186.2: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	C=	G	T
GRCh38.p14 chr 1	NC_000001.11:g.205836617=	NC_000001.11:g.205836617C>G	NC_000001.11:g.205836617C>T
GRCh37.p13 chr 1	NC_000001.10:g.205805745=	NC_000001.10:g.205805745C>G	NC_000001.10:g.205805745C>T
PM20D1 transcript variant 1	NM_152491.4:c.1116+3635=	NM_152491.4:c.1116+3635G>C	NM_152491.4:c.1116+3635G>A
PM20D1 transcript variant 1	NM_152491.5:c.1116+3635=	NM_152491.5:c.1116+3635G>C	NM_152491.5:c.1116+3635G>A

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#.

49 SubSNP, 18 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	WI_SSAHASNP	ss11412160	Jul 11, 2003 (116)
2	BGI	ss102815747	Dec 01, 2009 (131)
3	COMPLETE_GENOMICS	ss165722744	Jul 04, 2010 (132)
4	COMPLETE_GENOMICS	ss167454453	Jul 04, 2010 (132)
5	1000GENOMES	ss218842607	Jul 14, 2010 (132)
6	1000GENOMES	ss230871832	Jul 14, 2010 (132)
7	1000GENOMES	ss238490201	Jul 15, 2010 (132)
8	GMI	ss276188138	May 04, 2012 (137)
9	SSMP	ss648648523	Apr 25, 2013 (138)
10	EVA-GONL	ss976064455	Aug 21, 2014 (142)
11	JMKIDD_LAB	ss1068542940	Aug 21, 2014 (142)
12	1000GENOMES	ss1294349804	Aug 21, 2014 (142)
13	EVA_GENOME_DK	ss1574626202	Apr 01, 2015 (144)
14	EVA_DECODE	ss1585459632	Apr 01, 2015 (144)
15	EVA_UK10K_ALSPAC	ss1601977773	Apr 01, 2015 (144)
16	EVA_UK10K_TWINSUK	ss1644971806	Apr 01, 2015 (144)
17	WEILL_CORNELL_DGM	ss1919290684	Feb 12, 2016 (147)
18	GENOMED	ss1966954305	Jul 19, 2016 (147)
19	JJLAB	ss2020166334	Sep 14, 2016 (149)
20	USC_VALOUEV	ss2148196037	Dec 20, 2016 (150)
21	HUMAN_LONGEVITY	ss2169475971	Dec 20, 2016 (150)
22	SYSTEMSBIOZJU	ss2624592089	Nov 08, 2017 (151)
23	GRF	ss2698186612	Nov 08, 2017 (151)
24	GNOMAD	ss2765369233	Nov 08, 2017 (151)
25	SWEGEN	ss2988326738	Nov 08, 2017 (151)
26	BIOINF_KMB_FNS_UNIBA	ss3023843313	Nov 08, 2017 (151)
27	CSHL	ss3343876978	Nov 08, 2017 (151)
28	EGCUT_WGS	ss3656287075	Jul 12, 2019 (153)
29	EVA_DECODE	ss3688482395	Jul 12, 2019 (153)
30	ACPOP	ss3727796329	Jul 12, 2019 (153)
31	EVA	ss3747242367	Jul 12, 2019 (153)
32	KHV_HUMAN_GENOMES	ss3800248946	Jul 12, 2019 (153)
33	EVA	ss3826605682	Apr 25, 2020 (154)
34	SGDP_PRJ	ss3850742597	Apr 25, 2020 (154)
35	KRGDB	ss3896040463	Apr 25, 2020 (154)
36	TOPMED	ss4480926915	Apr 25, 2021 (155)
37	TOMMO_GENOMICS	ss5148093328	Apr 25, 2021 (155)
38	1000G_HIGH_COVERAGE	ss5245534518	Oct 12, 2022 (156)
39	EVA	ss5324310660	Oct 12, 2022 (156)
40	HUGCELL_USP	ss5445999444	Oct 12, 2022 (156)
41	EVA	ss5506162399	Oct 12, 2022 (156)
42	1000G_HIGH_COVERAGE	ss5519498047	Oct 12, 2022 (156)
43	SANFORD_IMAGENETICS	ss5627299005	Oct 12, 2022 (156)
44	TOMMO_GENOMICS	ss5675755733	Oct 12, 2022 (156)
45	YY_MCH	ss5801571982	Oct 12, 2022 (156)
46	EVA	ss5833157347	Oct 12, 2022 (156)
47	EVA	ss5849252628	Oct 12, 2022 (156)
48	EVA	ss5911671698	Oct 12, 2022 (156)
49	EVA	ss5939130485	Oct 12, 2022 (156)
50	1000Genomes	NC_000001.10 - 205805745	Oct 11, 2018 (152)
51	1000Genomes_30x	NC_000001.11 - 205836617	Oct 12, 2022 (156)
52	The Avon Longitudinal Study of Parents and Children	NC_000001.10 - 205805745	Oct 11, 2018 (152)
53	Genetic variation in the Estonian population	NC_000001.10 - 205805745	Oct 11, 2018 (152)
54	The Danish reference pan genome	NC_000001.10 - 205805745	Apr 25, 2020 (154)
55	gnomAD - Genomes	NC_000001.11 - 205836617	Apr 25, 2021 (155)
56	Genome of the Netherlands Release 5	NC_000001.10 - 205805745	Apr 25, 2020 (154)
57	KOREAN population from KRGDB	NC_000001.10 - 205805745	Apr 25, 2020 (154)
58	Northern Sweden	NC_000001.10 - 205805745	Jul 12, 2019 (153)
59	Qatari	NC_000001.10 - 205805745	Apr 25, 2020 (154)
60	SGDP_PRJ	NC_000001.10 - 205805745	Apr 25, 2020 (154)
61	Siberian	NC_000001.10 - 205805745	Apr 25, 2020 (154)
62	8.3KJPN	NC_000001.10 - 205805745	Apr 25, 2021 (155)
63	14KJPN	NC_000001.11 - 205836617	Oct 12, 2022 (156)
64	TopMed	NC_000001.11 - 205836617	Apr 25, 2021 (155)
65	UK 10K study - Twins	NC_000001.10 - 205805745	Oct 11, 2018 (152)
66	A Vietnamese Genetic Variation Database	NC_000001.10 - 205805745	Jul 12, 2019 (153)
67	ALFA	NC_000001.11 - 205836617	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
1160317757	NC_000001.11:205836616:C:G	NC_000001.11:205836616:C:G	(self)
ss165722744, ss167454453, ss276188138, ss1585459632	NC_000001.9:204072367:C:T	NC_000001.11:205836616:C:T	(self)
5193755, 2861113, 2025323, 1853785, 1249557, 3217857, 1081194, 1332614, 2759577, 712391, 6062635, 2861113, 617962, ss218842607, ss230871832, ss238490201, ss648648523, ss976064455, ss1068542940, ss1294349804, ss1574626202, ss1601977773, ss1644971806, ss1919290684, ss1966954305, ss2020166334, ss2148196037, ss2624592089, ss2698186612, ss2765369233, ss2988326738, ss3343876978, ss3656287075, ss3727796329, ss3747242367, ss3826605682, ss3850742597, ss3896040463, ss5148093328, ss5324310660, ss5506162399, ss5627299005, ss5833157347, ss5939130485	NC_000001.10:205805744:C:T	NC_000001.11:205836616:C:T	(self)
7023982, 37410285, 9592837, 44533250, 1160317757, ss2169475971, ss3023843313, ss3688482395, ss3800248946, ss4480926915, ss5245534518, ss5445999444, ss5519498047, ss5675755733, ss5801571982, ss5849252628, ss5911671698	NC_000001.11:205836616:C:T	NC_000001.11:205836616:C:T	(self)
ss102815747	NT_004487.19:57294386:C:T	NC_000001.11:205836616:C:T	(self)
ss11412160	NT_034410.4:2233172:C:T	NC_000001.11:205836616: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 rs7546846

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

rs7546846