Name: rs60148362
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.

rs60148362

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr1:35332599 (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=0.076894 (20353/264690, TOPMED)
T=0.057918 (8113/140078, GnomAD)
C=0.45994 (12997/28258, 14KJPN) (+ 15 more)
T=0.01135 (205/18066, ALFA)
C=0.46289 (7758/16760, 8.3KJPN)
T=0.1479 (947/6404, 1000G_30x)
T=0.1562 (782/5008, 1000G)
T=0.0232 (104/4480, Estonian)
T=0.0132 (51/3854, ALSPAC)
T=0.0146 (54/3708, TWINSUK)
C=0.4515 (1323/2930, KOREAN)
T=0.023 (23/998, GoNL)
T=0.032 (19/600, NorthernSweden)
T=0.019 (4/216, Qatari)
T=0.269 (57/212, Vietnamese)
C=0.418 (66/158, SGDP_PRJ)
T=0.03 (1/40, GENOME_DK)
C=0.40 (8/20, Siberian)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: ZMYM4 : 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	18066	C=0.98865	G=0.00000, T=0.01135
European	Sub	14134	C=0.99002	G=0.00000, T=0.00998
African	Sub	2716	C=0.9820	G=0.0000, T=0.0180
African Others	Sub	100	C=0.98	G=0.00, T=0.02
African American	Sub	2616	C=0.9820	G=0.0000, T=0.0180
Asian	Sub	40	C=0.97	G=0.00, T=0.03
East Asian	Sub	30	C=1.00	G=0.00, T=0.00
Other Asian	Sub	10	C=0.9	G=0.0, T=0.1
Latin American 1	Sub	130	C=1.000	G=0.000, T=0.000
Latin American 2	Sub	364	C=1.000	G=0.000, T=0.000
South Asian	Sub	76	C=1.00	G=0.00, T=0.00
Other	Sub	606	C=0.977	G=0.000, T=0.023

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=0.923106	T=0.076894
gnomAD - Genomes	Global	Study-wide	140078	C=0.942082	T=0.057918
gnomAD - Genomes	European	Sub	75908	C=0.98067	T=0.01933
gnomAD - Genomes	African	Sub	41976	C=0.93649	T=0.06351
gnomAD - Genomes	American	Sub	13616	C=0.82425	T=0.17575
gnomAD - Genomes	Ashkenazi Jewish	Sub	3316	C=0.9683	T=0.0317
gnomAD - Genomes	East Asian	Sub	3116	C=0.5770	T=0.4230
gnomAD - Genomes	Other	Sub	2146	C=0.9236	T=0.0764
14KJPN	JAPANESE	Study-wide	28258	C=0.45994	T=0.54006
Allele Frequency Aggregator	Total	Global	18066	C=0.98865	G=0.00000, T=0.01135
Allele Frequency Aggregator	European	Sub	14134	C=0.99002	G=0.00000, T=0.00998
Allele Frequency Aggregator	African	Sub	2716	C=0.9820	G=0.0000, T=0.0180
Allele Frequency Aggregator	Other	Sub	606	C=0.977	G=0.000, T=0.023
Allele Frequency Aggregator	Latin American 2	Sub	364	C=1.000	G=0.000, T=0.000
Allele Frequency Aggregator	Latin American 1	Sub	130	C=1.000	G=0.000, T=0.000
Allele Frequency Aggregator	South Asian	Sub	76	C=1.00	G=0.00, T=0.00
Allele Frequency Aggregator	Asian	Sub	40	C=0.97	G=0.00, T=0.03
8.3KJPN	JAPANESE	Study-wide	16760	C=0.46289	T=0.53711
1000Genomes_30x	Global	Study-wide	6404	C=0.8521	T=0.1479
1000Genomes_30x	African	Sub	1786	C=0.9295	T=0.0705
1000Genomes_30x	Europe	Sub	1266	C=0.9755	T=0.0245
1000Genomes_30x	South Asian	Sub	1202	C=0.9110	T=0.0890
1000Genomes_30x	East Asian	Sub	1170	C=0.5761	T=0.4239
1000Genomes_30x	American	Sub	980	C=0.809	T=0.191
1000Genomes	Global	Study-wide	5008	C=0.8438	T=0.1562
1000Genomes	African	Sub	1322	C=0.9274	T=0.0726
1000Genomes	East Asian	Sub	1008	C=0.5675	T=0.4325
1000Genomes	Europe	Sub	1006	C=0.9761	T=0.0239
1000Genomes	South Asian	Sub	978	C=0.908	T=0.092
1000Genomes	American	Sub	694	C=0.804	T=0.196
Genetic variation in the Estonian population	Estonian	Study-wide	4480	C=0.9768	T=0.0232
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	C=0.9868	T=0.0132
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	C=0.9854	T=0.0146
KOREAN population from KRGDB	KOREAN	Study-wide	2930	C=0.4515	T=0.5485
Genome of the Netherlands Release 5	Genome of the Netherlands	Study-wide	998	C=0.977	T=0.023
Northern Sweden	ACPOP	Study-wide	600	C=0.968	T=0.032
Qatari	Global	Study-wide	216	C=0.981	T=0.019
A Vietnamese Genetic Variation Database	Global	Study-wide	212	C=0.731	T=0.269
SGDP_PRJ	Global	Study-wide	158	C=0.418	T=0.582
The Danish reference pan genome	Danish	Study-wide	40	C=0.97	T=0.03
Siberian	Global	Study-wide	20	C=0.40	T=0.60

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.35332599C>G
GRCh38.p14 chr 1	NC_000001.11:g.35332599C>T
GRCh37.p13 chr 1	NC_000001.10:g.35798200C>G
GRCh37.p13 chr 1	NC_000001.10:g.35798200C>T

Gene: ZMYM4, zinc finger MYM-type containing 4 (plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
ZMYM4 transcript variant 2	NM_001350138.2:c.-12+7194… NM_001350138.2:c.-12+7194C>G	N/A	Intron Variant
ZMYM4 transcript variant 3	NM_001350139.2:c.-964+719… NM_001350139.2:c.-964+7194C>G	N/A	Intron Variant
ZMYM4 transcript variant 4	NM_001350140.2:c.-133+719… NM_001350140.2:c.-133+7194C>G	N/A	Intron Variant
ZMYM4 transcript variant 5	NM_001375653.1:c.94+7194C… NM_001375653.1:c.94+7194C>G	N/A	Intron Variant
ZMYM4 transcript variant 1	NM_005095.3:c.85+7194C>G	N/A	Intron Variant
ZMYM4 transcript variant X8	XM_005271331.3:c.-133+719… XM_005271331.3:c.-133+7194C>G	N/A	Intron Variant
ZMYM4 transcript variant X4	XM_017002803.2:c.-12+7194… XM_017002803.2:c.-12+7194C>G	N/A	Intron Variant
ZMYM4 transcript variant X9	XM_024450838.2:c.-133+719… XM_024450838.2:c.-133+7194C>G	N/A	Intron Variant
ZMYM4 transcript variant X1	XM_047434269.1:c.-11-2632… XM_047434269.1:c.-11-26326C>G	N/A	Intron Variant
ZMYM4 transcript variant X2	XM_047434270.1:c.-12+7194… XM_047434270.1:c.-12+7194C>G	N/A	Intron Variant
ZMYM4 transcript variant X3	XM_047434271.1:c.-12+7194… XM_047434271.1:c.-12+7194C>G	N/A	Intron Variant
ZMYM4 transcript variant X6	XM_047434276.1:c.94+7194C… XM_047434276.1:c.94+7194C>G	N/A	Intron Variant
ZMYM4 transcript variant X7	XM_047434278.1:c.-133+719… XM_047434278.1:c.-133+7194C>G	N/A	Intron Variant
ZMYM4 transcript variant X11	XM_047434282.1:c.-155+719… XM_047434282.1:c.-155+7194C>G	N/A	Intron Variant
ZMYM4 transcript variant X12	XM_047434289.1:c.-155+719… XM_047434289.1:c.-155+7194C>G	N/A	Intron Variant
ZMYM4 transcript variant X5	XM_047434274.1:c.	N/A	Genic Upstream Transcript Variant
ZMYM4 transcript variant X10	XM_047434279.1:c.	N/A	Genic Upstream Transcript Variant
ZMYM4 transcript variant X14	XR_007064889.1:n.	N/A	Intron Variant
ZMYM4 transcript variant X15	XR_007064890.1:n.	N/A	Intron Variant
ZMYM4 transcript variant X13	XR_246305.5: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.35332599=	NC_000001.11:g.35332599C>G	NC_000001.11:g.35332599C>T
GRCh37.p13 chr 1	NC_000001.10:g.35798200=	NC_000001.10:g.35798200C>G	NC_000001.10:g.35798200C>T
ZMYM4 transcript variant 2	NM_001350138.2:c.-12+7194=	NM_001350138.2:c.-12+7194C>G	NM_001350138.2:c.-12+7194C>T
ZMYM4 transcript variant 3	NM_001350139.2:c.-964+7194=	NM_001350139.2:c.-964+7194C>G	NM_001350139.2:c.-964+7194C>T
ZMYM4 transcript variant 4	NM_001350140.2:c.-133+7194=	NM_001350140.2:c.-133+7194C>G	NM_001350140.2:c.-133+7194C>T
ZMYM4 transcript variant 5	NM_001375653.1:c.94+7194=	NM_001375653.1:c.94+7194C>G	NM_001375653.1:c.94+7194C>T
ZMYM4 transcript variant 1	NM_005095.2:c.85+7194=	NM_005095.2:c.85+7194C>G	NM_005095.2:c.85+7194C>T
ZMYM4 transcript variant 1	NM_005095.3:c.85+7194=	NM_005095.3:c.85+7194C>G	NM_005095.3:c.85+7194C>T
ZMYM4 transcript variant X1	XM_005271328.1:c.94+7194=	XM_005271328.1:c.94+7194C>G	XM_005271328.1:c.94+7194C>T
ZMYM4 transcript variant X2	XM_005271329.1:c.94+7194=	XM_005271329.1:c.94+7194C>G	XM_005271329.1:c.94+7194C>T
ZMYM4 transcript variant X3	XM_005271330.1:c.76+7194=	XM_005271330.1:c.76+7194C>G	XM_005271330.1:c.76+7194C>T
ZMYM4 transcript variant X9	XM_005271331.1:c.-133+7194=	XM_005271331.1:c.-133+7194C>G	XM_005271331.1:c.-133+7194C>T
ZMYM4 transcript variant X8	XM_005271331.3:c.-133+7194=	XM_005271331.3:c.-133+7194C>G	XM_005271331.3:c.-133+7194C>T
ZMYM4 transcript variant X4	XM_017002803.2:c.-12+7194=	XM_017002803.2:c.-12+7194C>G	XM_017002803.2:c.-12+7194C>T
ZMYM4 transcript variant X9	XM_024450838.2:c.-133+7194=	XM_024450838.2:c.-133+7194C>G	XM_024450838.2:c.-133+7194C>T
ZMYM4 transcript variant X1	XM_047434269.1:c.-11-26326=	XM_047434269.1:c.-11-26326C>G	XM_047434269.1:c.-11-26326C>T
ZMYM4 transcript variant X2	XM_047434270.1:c.-12+7194=	XM_047434270.1:c.-12+7194C>G	XM_047434270.1:c.-12+7194C>T
ZMYM4 transcript variant X3	XM_047434271.1:c.-12+7194=	XM_047434271.1:c.-12+7194C>G	XM_047434271.1:c.-12+7194C>T
ZMYM4 transcript variant X6	XM_047434276.1:c.94+7194=	XM_047434276.1:c.94+7194C>G	XM_047434276.1:c.94+7194C>T
ZMYM4 transcript variant X7	XM_047434278.1:c.-133+7194=	XM_047434278.1:c.-133+7194C>G	XM_047434278.1:c.-133+7194C>T
ZMYM4 transcript variant X11	XM_047434282.1:c.-155+7194=	XM_047434282.1:c.-155+7194C>G	XM_047434282.1:c.-155+7194C>T
ZMYM4 transcript variant X12	XM_047434289.1:c.-155+7194=	XM_047434289.1:c.-155+7194C>G	XM_047434289.1:c.-155+7194C>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#.

46 SubSNP, 18 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	HGSV	ss84075103	Dec 15, 2007 (129)
2	BGI	ss105141688	Dec 01, 2009 (131)
3	GMI	ss154865497	Dec 01, 2009 (131)
4	BUSHMAN	ss198290805	Jul 04, 2010 (132)
5	1000GENOMES	ss218323159	Jul 14, 2010 (132)
6	1000GENOMES	ss230490182	Jul 14, 2010 (132)
7	1000GENOMES	ss238192866	Jul 15, 2010 (132)
8	GMI	ss275781545	May 04, 2012 (137)
9	SSMP	ss647751369	Apr 25, 2013 (138)
10	EVA-GONL	ss975030353	Aug 21, 2014 (142)
11	JMKIDD_LAB	ss1067792327	Aug 21, 2014 (142)
12	1000GENOMES	ss1290366023	Aug 21, 2014 (142)
13	EVA_GENOME_DK	ss1573985805	Apr 01, 2015 (144)
14	EVA_DECODE	ss1584390307	Apr 01, 2015 (144)
15	EVA_UK10K_ALSPAC	ss1599898972	Apr 01, 2015 (144)
16	EVA_UK10K_TWINSUK	ss1642893005	Apr 01, 2015 (144)
17	HAMMER_LAB	ss1794173144	Sep 08, 2015 (146)
18	WEILL_CORNELL_DGM	ss1918241268	Feb 12, 2016 (147)
19	GENOMED	ss1966720640	Jul 19, 2016 (147)
20	JJLAB	ss2019632314	Sep 14, 2016 (149)
21	USC_VALOUEV	ss2147642573	Dec 20, 2016 (150)
22	HUMAN_LONGEVITY	ss2161409463	Dec 20, 2016 (150)
23	SYSTEMSBIOZJU	ss2624332402	Nov 08, 2017 (151)
24	GRF	ss2697550229	Nov 08, 2017 (151)
25	GNOMAD	ss2753630681	Nov 08, 2017 (151)
26	SWEGEN	ss2986602950	Nov 08, 2017 (151)
27	EGCUT_WGS	ss3654666656	Jul 12, 2019 (153)
28	EVA_DECODE	ss3686512561	Jul 12, 2019 (153)
29	ACPOP	ss3726937049	Jul 12, 2019 (153)
30	EVA	ss3746041077	Jul 12, 2019 (153)
31	KHV_HUMAN_GENOMES	ss3799057819	Jul 12, 2019 (153)
32	SGDP_PRJ	ss3848580128	Apr 25, 2020 (154)
33	KRGDB	ss3893534361	Apr 25, 2020 (154)
34	TOPMED	ss4445035302	Apr 25, 2021 (155)
35	TOMMO_GENOMICS	ss5143328891	Apr 25, 2021 (155)
36	1000G_HIGH_COVERAGE	ss5241807168	Oct 17, 2022 (156)
37	EVA	ss5317878029	Oct 17, 2022 (156)
38	HUGCELL_USP	ss5442923618	Oct 17, 2022 (156)
39	1000G_HIGH_COVERAGE	ss5513855562	Oct 17, 2022 (156)
40	SANFORD_IMAGENETICS	ss5625274534	Oct 17, 2022 (156)
41	TOMMO_GENOMICS	ss5667901604	Oct 17, 2022 (156)
42	YY_MCH	ss5800482741	Oct 17, 2022 (156)
43	EVA	ss5831784134	Oct 17, 2022 (156)
44	EVA	ss5848855142	Oct 17, 2022 (156)
45	EVA	ss5907729742	Oct 17, 2022 (156)
46	EVA	ss5937093657	Oct 17, 2022 (156)
47	1000Genomes	NC_000001.10 - 35798200	Oct 11, 2018 (152)
48	1000Genomes_30x	NC_000001.11 - 35332599	Oct 17, 2022 (156)
49	The Avon Longitudinal Study of Parents and Children	NC_000001.10 - 35798200	Oct 11, 2018 (152)
50	Genetic variation in the Estonian population	NC_000001.10 - 35798200	Oct 11, 2018 (152)
51	The Danish reference pan genome	NC_000001.10 - 35798200	Apr 25, 2020 (154)
52	gnomAD - Genomes	NC_000001.11 - 35332599	Apr 25, 2021 (155)
53	Genome of the Netherlands Release 5	NC_000001.10 - 35798200	Apr 25, 2020 (154)
54	KOREAN population from KRGDB	NC_000001.10 - 35798200	Apr 25, 2020 (154)
55	Northern Sweden	NC_000001.10 - 35798200	Jul 12, 2019 (153)
56	Qatari	NC_000001.10 - 35798200	Apr 25, 2020 (154)
57	SGDP_PRJ	NC_000001.10 - 35798200	Apr 25, 2020 (154)
58	Siberian	NC_000001.10 - 35798200	Apr 25, 2020 (154)
59	8.3KJPN	NC_000001.10 - 35798200	Apr 25, 2021 (155)
60	14KJPN	NC_000001.11 - 35332599	Oct 17, 2022 (156)
61	TopMed	NC_000001.11 - 35332599	Apr 25, 2021 (155)
62	UK 10K study - Twins	NC_000001.10 - 35798200	Oct 11, 2018 (152)
63	A Vietnamese Genetic Variation Database	NC_000001.10 - 35798200	Jul 12, 2019 (153)
64	ALFA	NC_000001.11 - 35332599	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
15814348141	NC_000001.11:35332598:C:G	NC_000001.11:35332598:C:G	(self)
ss84075103	NC_000001.8:35467292:C:T	NC_000001.11:35332598:C:T	(self)
ss198290805, ss275781545, ss1584390307	NC_000001.9:35570786:C:T	NC_000001.11:35332598:C:T	(self)
1065617, 573579, 404904, 1455063, 246526, 711755, 221914, 283198, 597108, 158927, 1298198, 573579, 118188, ss218323159, ss230490182, ss238192866, ss647751369, ss975030353, ss1067792327, ss1290366023, ss1573985805, ss1599898972, ss1642893005, ss1794173144, ss1918241268, ss1966720640, ss2019632314, ss2147642573, ss2624332402, ss2697550229, ss2753630681, ss2986602950, ss3654666656, ss3726937049, ss3746041077, ss3848580128, ss3893534361, ss5143328891, ss5317878029, ss5625274534, ss5831784134, ss5937093657	NC_000001.10:35798199:C:T	NC_000001.11:35332598:C:T	(self)
1381497, 7501879, 1738708, 8641637, 15814348141, ss2161409463, ss3686512561, ss3799057819, ss4445035302, ss5241807168, ss5442923618, ss5513855562, ss5667901604, ss5800482741, ss5848855142, ss5907729742	NC_000001.11:35332598:C:T	NC_000001.11:35332598:C:T	(self)
ss105141688, ss154865497	NT_032977.9:5770117:C:T	NC_000001.11:35332598: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 rs60148362

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.

Choose placement

dbSNP Short Genetic Variations

Welcome to the Reference SNP (rs) Report

Reference SNP (rs) Report

rs60148362