Name: rs6007949
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.

rs6007949

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr22:46650529 (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: G=0.157430 (22061/140132, GnomAD)
G=0.05303 (855/16122, ALFA)
G=0.1273 (815/6404, 1000G_30x) (+ 12 more)
G=0.1232 (617/5008, 1000G)
G=0.0831 (372/4476, Estonian)
G=0.0919 (354/3854, ALSPAC)
G=0.0998 (370/3708, TWINSUK)
G=0.0005 (1/1832, Korea1K)
G=0.106 (106/998, GoNL)
G=0.087 (52/600, NorthernSweden)
G=0.204 (44/216, Qatari)
C=0.41 (31/76, SGDP_PRJ)
G=0.07 (3/40, GENOME_DK)
C=0.5 (4/8, Siberian)
G=0.5 (4/8, Siberian)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: GRAMD4 : 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	16122	C=0.94697	G=0.05303, T=0.00000
European	Sub	13006	C=0.95241	G=0.04759, T=0.00000
African	Sub	1694	C=0.8796	G=0.1204, T=0.0000
African Others	Sub	60	C=0.90	G=0.10, T=0.00
African American	Sub	1634	C=0.8788	G=0.1212, T=0.0000
Asian	Sub	112	C=1.000	G=0.000, T=0.000
East Asian	Sub	86	C=1.00	G=0.00, T=0.00
Other Asian	Sub	26	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	540	C=1.000	G=0.000, T=0.000
South Asian	Sub	90	C=1.00	G=0.00, T=0.00
Other	Sub	566	C=0.943	G=0.057, T=0.000

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").

Download

Study	Population	Group	Sample Size	Ref Allele	Alt Allele
gnomAD - Genomes	Global	Study-wide	140132	C=0.842570	G=0.157430
gnomAD - Genomes	European	Sub	75904	C=0.91002	G=0.08998
gnomAD - Genomes	African	Sub	41962	C=0.68433	G=0.31567
gnomAD - Genomes	American	Sub	13658	C=0.89999	G=0.10001
gnomAD - Genomes	Ashkenazi Jewish	Sub	3324	C=0.8992	G=0.1008
gnomAD - Genomes	East Asian	Sub	3134	C=0.9994	G=0.0006
gnomAD - Genomes	Other	Sub	2150	C=0.8688	G=0.1312
Allele Frequency Aggregator	Total	Global	16122	C=0.94697	G=0.05303, T=0.00000
Allele Frequency Aggregator	European	Sub	13006	C=0.95241	G=0.04759, T=0.00000
Allele Frequency Aggregator	African	Sub	1694	C=0.8796	G=0.1204, T=0.0000
Allele Frequency Aggregator	Other	Sub	566	C=0.943	G=0.057, T=0.000
Allele Frequency Aggregator	Latin American 2	Sub	540	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	Asian	Sub	112	C=1.000	G=0.000, T=0.000
Allele Frequency Aggregator	South Asian	Sub	90	C=1.00	G=0.00, T=0.00
1000Genomes_30x	Global	Study-wide	6404	C=0.8726	G=0.1273, T=0.0002
1000Genomes_30x	African	Sub	1786	C=0.6753	G=0.3247, T=0.0000
1000Genomes_30x	Europe	Sub	1266	C=0.9155	G=0.0845, T=0.0000
1000Genomes_30x	South Asian	Sub	1202	C=0.9676	G=0.0316, T=0.0008
1000Genomes_30x	East Asian	Sub	1170	C=0.9991	G=0.0009, T=0.0000
1000Genomes_30x	American	Sub	980	C=0.909	G=0.091, T=0.000
1000Genomes	Global	Study-wide	5008	C=0.8768	G=0.1232
1000Genomes	African	Sub	1322	C=0.6694	G=0.3306
1000Genomes	East Asian	Sub	1008	C=0.9990	G=0.0010
1000Genomes	Europe	Sub	1006	C=0.9145	G=0.0855
1000Genomes	South Asian	Sub	978	C=0.969	G=0.031
1000Genomes	American	Sub	694	C=0.909	G=0.091
Genetic variation in the Estonian population	Estonian	Study-wide	4476	C=0.9169	G=0.0831
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	C=0.9081	G=0.0919
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	C=0.9002	G=0.0998
Korean Genome Project	KOREAN	Study-wide	1832	C=0.9995	G=0.0005
Genome of the Netherlands Release 5	Genome of the Netherlands	Study-wide	998	C=0.894	G=0.106
Northern Sweden	ACPOP	Study-wide	600	C=0.913	G=0.087
Qatari	Global	Study-wide	216	C=0.796	G=0.204
SGDP_PRJ	Global	Study-wide	76	C=0.41	G=0.59
The Danish reference pan genome	Danish	Study-wide	40	C=0.93	G=0.07
Siberian	Global	Study-wide	8	C=0.5	G=0.5

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 22	NC_000022.11:g.46650529C>G
GRCh38.p14 chr 22	NC_000022.11:g.46650529C>T
GRCh37.p13 chr 22	NC_000022.10:g.47046426C>G
GRCh37.p13 chr 22	NC_000022.10:g.47046426C>T

Gene: GRAMD4, GRAM domain containing 4 (plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
GRAMD4 transcript variant 2	NM_001366660.1:c.362-7658… NM_001366660.1:c.362-7658C>G	N/A	Intron Variant
GRAMD4 transcript variant 1	NM_015124.5:c.284-7658C>G	N/A	Intron Variant
GRAMD4 transcript variant X2	XM_005261396.4:c.362-7658… XM_005261396.4:c.362-7658C>G	N/A	Intron Variant
GRAMD4 transcript variant X3	XM_006724169.2:c.353-7658… XM_006724169.2:c.353-7658C>G	N/A	Intron Variant
GRAMD4 transcript variant X5	XM_006724170.5:c.284-7658… XM_006724170.5:c.284-7658C>G	N/A	Intron Variant
GRAMD4 transcript variant X12	XM_011530011.2:c.284-7658… XM_011530011.2:c.284-7658C>G	N/A	Intron Variant
GRAMD4 transcript variant X13	XM_011530012.2:c.284-7658… XM_011530012.2:c.284-7658C>G	N/A	Intron Variant
GRAMD4 transcript variant X14	XM_011530014.2:c.284-7658… XM_011530014.2:c.284-7658C>G	N/A	Intron Variant
GRAMD4 transcript variant X10	XM_017028670.3:c.284-7658… XM_017028670.3:c.284-7658C>G	N/A	Intron Variant
GRAMD4 transcript variant X1	XM_047441205.1:c.371-7658… XM_047441205.1:c.371-7658C>G	N/A	Intron Variant
GRAMD4 transcript variant X4	XM_047441206.1:c.362-7658… XM_047441206.1:c.362-7658C>G	N/A	Intron Variant
GRAMD4 transcript variant X6	XM_047441207.1:c.284-7658… XM_047441207.1:c.284-7658C>G	N/A	Intron Variant
GRAMD4 transcript variant X7	XM_047441208.1:c.284-7658… XM_047441208.1:c.284-7658C>G	N/A	Intron Variant
GRAMD4 transcript variant X8	XM_047441209.1:c.284-7658… XM_047441209.1:c.284-7658C>G	N/A	Intron Variant
GRAMD4 transcript variant X9	XM_047441210.1:c.284-7658… XM_047441210.1:c.284-7658C>G	N/A	Intron Variant
GRAMD4 transcript variant X11	XM_047441211.1:c.284-7658… XM_047441211.1:c.284-7658C>G	N/A	Intron Variant
GRAMD4 transcript variant X15	XM_047441212.1:c.-42+516C… XM_047441212.1:c.-42+516C>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	T
GRCh38.p14 chr 22	NC_000022.11:g.46650529=	NC_000022.11:g.46650529C>G	NC_000022.11:g.46650529C>T
GRCh37.p13 chr 22	NC_000022.10:g.47046426=	NC_000022.10:g.47046426C>G	NC_000022.10:g.47046426C>T
GRAMD4 transcript variant 2	NM_001366660.1:c.362-7658=	NM_001366660.1:c.362-7658C>G	NM_001366660.1:c.362-7658C>T
GRAMD4 transcript	NM_015124.3:c.284-7658=	NM_015124.3:c.284-7658C>G	NM_015124.3:c.284-7658C>T
GRAMD4 transcript variant 1	NM_015124.5:c.284-7658=	NM_015124.5:c.284-7658C>G	NM_015124.5:c.284-7658C>T
GRAMD4 transcript variant X1	XM_005261396.1:c.362-7658=	XM_005261396.1:c.362-7658C>G	XM_005261396.1:c.362-7658C>T
GRAMD4 transcript variant X2	XM_005261396.4:c.362-7658=	XM_005261396.4:c.362-7658C>G	XM_005261396.4:c.362-7658C>T
GRAMD4 transcript variant X2	XM_005261397.1:c.362-7658=	XM_005261397.1:c.362-7658C>G	XM_005261397.1:c.362-7658C>T
GRAMD4 transcript variant X6	XM_005261398.1:c.284-7658=	XM_005261398.1:c.284-7658C>G	XM_005261398.1:c.284-7658C>T
GRAMD4 transcript variant X4	XM_005261399.1:c.284-7658=	XM_005261399.1:c.284-7658C>G	XM_005261399.1:c.284-7658C>T
GRAMD4 transcript variant X5	XM_005261400.1:c.362-7658=	XM_005261400.1:c.362-7658C>G	XM_005261400.1:c.362-7658C>T
GRAMD4 transcript variant X6	XM_005261401.1:c.284-7658=	XM_005261401.1:c.284-7658C>G	XM_005261401.1:c.284-7658C>T
GRAMD4 transcript variant X3	XM_006724169.2:c.353-7658=	XM_006724169.2:c.353-7658C>G	XM_006724169.2:c.353-7658C>T
GRAMD4 transcript variant X5	XM_006724170.5:c.284-7658=	XM_006724170.5:c.284-7658C>G	XM_006724170.5:c.284-7658C>T
GRAMD4 transcript variant X12	XM_011530011.2:c.284-7658=	XM_011530011.2:c.284-7658C>G	XM_011530011.2:c.284-7658C>T
GRAMD4 transcript variant X13	XM_011530012.2:c.284-7658=	XM_011530012.2:c.284-7658C>G	XM_011530012.2:c.284-7658C>T
GRAMD4 transcript variant X14	XM_011530014.2:c.284-7658=	XM_011530014.2:c.284-7658C>G	XM_011530014.2:c.284-7658C>T
GRAMD4 transcript variant X10	XM_017028670.3:c.284-7658=	XM_017028670.3:c.284-7658C>G	XM_017028670.3:c.284-7658C>T
GRAMD4 transcript variant X1	XM_047441205.1:c.371-7658=	XM_047441205.1:c.371-7658C>G	XM_047441205.1:c.371-7658C>T
GRAMD4 transcript variant X4	XM_047441206.1:c.362-7658=	XM_047441206.1:c.362-7658C>G	XM_047441206.1:c.362-7658C>T
GRAMD4 transcript variant X6	XM_047441207.1:c.284-7658=	XM_047441207.1:c.284-7658C>G	XM_047441207.1:c.284-7658C>T
GRAMD4 transcript variant X7	XM_047441208.1:c.284-7658=	XM_047441208.1:c.284-7658C>G	XM_047441208.1:c.284-7658C>T
GRAMD4 transcript variant X8	XM_047441209.1:c.284-7658=	XM_047441209.1:c.284-7658C>G	XM_047441209.1:c.284-7658C>T
GRAMD4 transcript variant X9	XM_047441210.1:c.284-7658=	XM_047441210.1:c.284-7658C>G	XM_047441210.1:c.284-7658C>T
GRAMD4 transcript variant X11	XM_047441211.1:c.284-7658=	XM_047441211.1:c.284-7658C>G	XM_047441211.1:c.284-7658C>T
GRAMD4 transcript variant X15	XM_047441212.1:c.-42+516=	XM_047441212.1:c.-42+516C>G	XM_047441212.1:c.-42+516C>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, 16 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	SC_SNP	ss8305878	Apr 21, 2003 (114)
2	ABI	ss44331166	Mar 15, 2006 (126)
3	HUMANGENOME_JCVI	ss96130388	Feb 05, 2009 (130)
4	1000GENOMES	ss114313998	Jan 25, 2009 (130)
5	ENSEMBL	ss143274385	Dec 01, 2009 (131)
6	COMPLETE_GENOMICS	ss168100744	Jul 04, 2010 (132)
7	COMPLETE_GENOMICS	ss169487748	Jul 04, 2010 (132)
8	1000GENOMES	ss228720324	Jul 14, 2010 (132)
9	1000GENOMES	ss238097385	Jul 15, 2010 (132)
10	TISHKOFF	ss566694649	Apr 25, 2013 (138)
11	EVA-GONL	ss995434630	Aug 21, 2014 (142)
12	JMKIDD_LAB	ss1082716384	Aug 21, 2014 (142)
13	1000GENOMES	ss1367488952	Aug 21, 2014 (142)
14	DDI	ss1429281468	Apr 01, 2015 (144)
15	EVA_GENOME_DK	ss1579783218	Apr 01, 2015 (144)
16	EVA_UK10K_ALSPAC	ss1640162885	Apr 01, 2015 (144)
17	EVA_UK10K_TWINSUK	ss1683156918	Apr 01, 2015 (144)
18	EVA_DECODE	ss1699505750	Apr 01, 2015 (144)
19	HAMMER_LAB	ss1809825556	Sep 08, 2015 (146)
20	WEILL_CORNELL_DGM	ss1939006127	Feb 12, 2016 (147)
21	JJLAB	ss2030275184	Sep 14, 2016 (149)
22	USC_VALOUEV	ss2158898397	Dec 20, 2016 (150)
23	HUMAN_LONGEVITY	ss2247990538	Dec 20, 2016 (150)
24	GNOMAD	ss2975320876	Nov 08, 2017 (151)
25	SWEGEN	ss3019439390	Nov 08, 2017 (151)
26	BIOINF_KMB_FNS_UNIBA	ss3028974265	Nov 08, 2017 (151)
27	CSHL	ss3352875474	Nov 08, 2017 (151)
28	URBANLAB	ss3651195655	Oct 12, 2018 (152)
29	EGCUT_WGS	ss3685928954	Jul 13, 2019 (153)
30	ACPOP	ss3744004035	Jul 13, 2019 (153)
31	EVA	ss3759483113	Jul 13, 2019 (153)
32	PACBIO	ss3793710813	Jul 13, 2019 (153)
33	PACBIO	ss3798597335	Jul 13, 2019 (153)
34	KHV_HUMAN_GENOMES	ss3822641199	Jul 13, 2019 (153)
35	EVA	ss3836033030	Apr 27, 2020 (154)
36	SGDP_PRJ	ss3890724492	Apr 27, 2020 (154)
37	KOGIC	ss3983817061	Apr 27, 2020 (154)
38	TOPMED	ss5112054394	Apr 27, 2021 (155)
39	TOPMED	ss5112054395	Apr 27, 2021 (155)
40	1000G_HIGH_COVERAGE	ss5311393448	Oct 16, 2022 (156)
41	EVA	ss5441837422	Oct 16, 2022 (156)
42	1000G_HIGH_COVERAGE	ss5619081696	Oct 16, 2022 (156)
43	SANFORD_IMAGENETICS	ss5664654517	Oct 16, 2022 (156)
44	EVA	ss5822186499	Oct 16, 2022 (156)
45	EVA	ss5882147643	Oct 16, 2022 (156)
46	EVA	ss5959513014	Oct 16, 2022 (156)
47	1000Genomes	NC_000022.10 - 47046426	Oct 12, 2018 (152)
48	1000Genomes_30x	NC_000022.11 - 46650529	Oct 16, 2022 (156)
49	The Avon Longitudinal Study of Parents and Children	NC_000022.10 - 47046426	Oct 12, 2018 (152)
50	Genetic variation in the Estonian population	NC_000022.10 - 47046426	Oct 12, 2018 (152)
51	The Danish reference pan genome	NC_000022.10 - 47046426	Apr 27, 2020 (154)
52	gnomAD - Genomes	NC_000022.11 - 46650529	Apr 27, 2021 (155)
53	Genome of the Netherlands Release 5	NC_000022.10 - 47046426	Apr 27, 2020 (154)
54	Korean Genome Project	NC_000022.11 - 46650529	Apr 27, 2020 (154)
55	Northern Sweden	NC_000022.10 - 47046426	Jul 13, 2019 (153)
56	Qatari	NC_000022.10 - 47046426	Apr 27, 2020 (154)
57	SGDP_PRJ	NC_000022.10 - 47046426	Apr 27, 2020 (154)
58	Siberian	NC_000022.10 - 47046426	Apr 27, 2020 (154)
59	TopMed Submission ignored due to conflicting rows: Row 387163341 (NC_000022.11:46650528:C:G 42650/264690) Row 387163342 (NC_000022.11:46650528:C:T 1/264690)	-	Apr 27, 2021 (155)
60	TopMed Submission ignored due to conflicting rows: Row 387163341 (NC_000022.11:46650528:C:G 42650/264690) Row 387163342 (NC_000022.11:46650528:C:T 1/264690)	-	Apr 27, 2021 (155)
61	UK 10K study - Twins	NC_000022.10 - 47046426	Oct 12, 2018 (152)
62	ALFA	NC_000022.11 - 46650529	Apr 27, 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
ss114313998, ss168100744, ss169487748, ss1699505750	NC_000022.9:45425089:C:G	NC_000022.11:46650528:C:G	(self)
81052724, 44834605, 31667202, 5948157, 19974325, 17288900, 21048049, 42741472, 11414751, 44834605, ss228720324, ss238097385, ss566694649, ss995434630, ss1082716384, ss1367488952, ss1429281468, ss1579783218, ss1640162885, ss1683156918, ss1809825556, ss1939006127, ss2030275184, ss2158898397, ss2975320876, ss3019439390, ss3352875474, ss3685928954, ss3744004035, ss3759483113, ss3793710813, ss3798597335, ss3836033030, ss3890724492, ss5441837422, ss5664654517, ss5822186499, ss5959513014	NC_000022.10:47046425:C:G	NC_000022.11:46650528:C:G	(self)
106607631, 572337247, 40195062, 9802246576, ss2247990538, ss3028974265, ss3651195655, ss3822641199, ss3983817061, ss5112054394, ss5311393448, ss5619081696, ss5882147643	NC_000022.11:46650528:C:G	NC_000022.11:46650528:C:G	(self)
ss8305878, ss44331166, ss96130388, ss143274385	NT_011520.12:26436994:C:G	NC_000022.11:46650528:C:G	(self)
106607631, 9802246576, ss5112054395, ss5619081696	NC_000022.11:46650528:C:T	NC_000022.11:46650528: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 rs6007949

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

rs6007949