Name: rs2507972
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.

rs2507972

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr6:31397273 (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>T
Variation Type: SNV Single Nucleotide Variation
Frequency: T=0.052133 (13799/264690, TOPMED)
T=0.051994 (7099/136536, GnomAD)
T=0.06254 (2239/35802, ALFA) (+ 12 more)
T=0.19419 (5484/28240, 14KJPN)
T=0.19793 (3315/16748, 8.3KJPN)
T=0.0686 (439/6404, 1000G_30x)
T=0.0911 (456/5008, 1000G)
T=0.1263 (369/2922, KOREAN)
T=0.1699 (192/1130, Daghestan)
T=0.070 (70/998, GoNL)
T=0.048 (29/600, NorthernSweden)
T=0.199 (43/216, Qatari)
C=0.45 (43/96, SGDP_PRJ)
C=0.5 (2/4, Siberian)
T=0.5 (2/4, Siberian)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: MICA-AS1 : 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	35802	C=0.93746	T=0.06254
European	Sub	30426	C=0.93177	T=0.06823
African	Sub	3376	C=0.9884	T=0.0116
African Others	Sub	114	C=1.000	T=0.000
African American	Sub	3262	C=0.9880	T=0.0120
Asian	Sub	158	C=0.924	T=0.076
East Asian	Sub	132	C=0.917	T=0.083
Other Asian	Sub	26	C=0.96	T=0.04
Latin American 1	Sub	146	C=0.911	T=0.089
Latin American 2	Sub	610	C=0.952	T=0.048
South Asian	Sub	100	C=0.87	T=0.13
Other	Sub	986	C=0.942	T=0.058

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=0.947867	T=0.052133
gnomAD - Genomes	Global	Study-wide	136536	C=0.948006	T=0.051994
gnomAD - Genomes	European	Sub	74440	C=0.93242	T=0.06758
gnomAD - Genomes	African	Sub	40446	C=0.98742	T=0.01258
gnomAD - Genomes	American	Sub	13258	C=0.93755	T=0.06245
gnomAD - Genomes	Ashkenazi Jewish	Sub	3260	C=0.8920	T=0.1080
gnomAD - Genomes	East Asian	Sub	3022	C=0.9282	T=0.0718
gnomAD - Genomes	Other	Sub	2110	C=0.9232	T=0.0768
Allele Frequency Aggregator	Total	Global	35802	C=0.93746	T=0.06254
Allele Frequency Aggregator	European	Sub	30426	C=0.93177	T=0.06823
Allele Frequency Aggregator	African	Sub	3376	C=0.9884	T=0.0116
Allele Frequency Aggregator	Other	Sub	986	C=0.942	T=0.058
Allele Frequency Aggregator	Latin American 2	Sub	610	C=0.952	T=0.048
Allele Frequency Aggregator	Asian	Sub	158	C=0.924	T=0.076
Allele Frequency Aggregator	Latin American 1	Sub	146	C=0.911	T=0.089
Allele Frequency Aggregator	South Asian	Sub	100	C=0.87	T=0.13
14KJPN	JAPANESE	Study-wide	28240	C=0.80581	T=0.19419
8.3KJPN	JAPANESE	Study-wide	16748	C=0.80207	T=0.19793
1000Genomes_30x	Global	Study-wide	6404	C=0.9314	T=0.0686
1000Genomes_30x	African	Sub	1786	C=0.9950	T=0.0050
1000Genomes_30x	Europe	Sub	1266	C=0.9147	T=0.0853
1000Genomes_30x	South Asian	Sub	1202	C=0.8661	T=0.1339
1000Genomes_30x	East Asian	Sub	1170	C=0.9145	T=0.0855
1000Genomes_30x	American	Sub	980	C=0.938	T=0.062
1000Genomes	Global	Study-wide	5008	C=0.9089	T=0.0911
1000Genomes	African	Sub	1322	C=0.9735	T=0.0265
1000Genomes	East Asian	Sub	1008	C=0.8909	T=0.1091
1000Genomes	Europe	Sub	1006	C=0.9056	T=0.0944
1000Genomes	South Asian	Sub	978	C=0.851	T=0.149
1000Genomes	American	Sub	694	C=0.899	T=0.101
KOREAN population from KRGDB	KOREAN	Study-wide	2922	C=0.8737	T=0.1263
Genome-wide autozygosity in Daghestan	Global	Study-wide	1130	C=0.8301	T=0.1699
Genome-wide autozygosity in Daghestan	Daghestan	Sub	626	C=0.788	T=0.212
Genome-wide autozygosity in Daghestan	Near_East	Sub	142	C=0.873	T=0.127
Genome-wide autozygosity in Daghestan	Central Asia	Sub	122	C=0.852	T=0.148
Genome-wide autozygosity in Daghestan	Europe	Sub	108	C=0.935	T=0.065
Genome-wide autozygosity in Daghestan	South Asian	Sub	96	C=0.92	T=0.08
Genome-wide autozygosity in Daghestan	Caucasus	Sub	36	C=0.78	T=0.22
Genome of the Netherlands Release 5	Genome of the Netherlands	Study-wide	998	C=0.930	T=0.070
Northern Sweden	ACPOP	Study-wide	600	C=0.952	T=0.048
Qatari	Global	Study-wide	216	C=0.801	T=0.199
SGDP_PRJ	Global	Study-wide	96	C=0.45	T=0.55
Siberian	Global	Study-wide	4	C=0.5	T=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 6	NC_000006.12:g.31397273C>T
GRCh37.p13 chr 6	NC_000006.11:g.31365050C>T
MICA RefSeqGene	NG_034139.1:g.2495C>T
GRCh38.p14 chr 6 alt locus HSCHR6_MHC_COX_CTG1	NT_113891.3:g.2877641C>T
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_COX_CTG1	NT_113891.2:g.2877747C>T
GRCh38.p14 chr 6 alt locus HSCHR6_MHC_QBL_CTG1	NT_167248.2:g.2652905C>T
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_QBL_CTG1	NT_167248.1:g.2658501C>T
GRCh38.p14 chr 6 alt locus HSCHR6_MHC_SSTO_CTG1	NT_167249.2:g.2699553C>T
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_SSTO_CTG1	NT_167249.1:g.2698851C>T
GRCh38.p14 chr 6 alt locus HSCHR6_MHC_MANN_CTG1	NT_167246.2:g.2705874C>T
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_MANN_CTG1	NT_167246.1:g.2711494C>T

Gene: MICA-AS1, MICA antisense RNA 1 (minus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
MICA-AS1 transcript variant 1	NR_148222.1:n.	N/A	Intron Variant
MICA-AS1 transcript variant 2	NR_148223.1: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	C=	T
GRCh38.p14 chr 6	NC_000006.12:g.31397273=	NC_000006.12:g.31397273C>T
GRCh37.p13 chr 6	NC_000006.11:g.31365050=	NC_000006.11:g.31365050C>T
MICA RefSeqGene	NG_034139.1:g.2495=	NG_034139.1:g.2495C>T
GRCh38.p14 chr 6 alt locus HSCHR6_MHC_COX_CTG1	NT_113891.3:g.2877641=	NT_113891.3:g.2877641C>T
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_COX_CTG1	NT_113891.2:g.2877747=	NT_113891.2:g.2877747C>T
GRCh38.p14 chr 6 alt locus HSCHR6_MHC_QBL_CTG1	NT_167248.2:g.2652905=	NT_167248.2:g.2652905C>T
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_QBL_CTG1	NT_167248.1:g.2658501=	NT_167248.1:g.2658501C>T
GRCh38.p14 chr 6 alt locus HSCHR6_MHC_SSTO_CTG1	NT_167249.2:g.2699553=	NT_167249.2:g.2699553C>T
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_SSTO_CTG1	NT_167249.1:g.2698851=	NT_167249.1:g.2698851C>T
GRCh38.p14 chr 6 alt locus HSCHR6_MHC_MANN_CTG1	NT_167246.2:g.2705874=	NT_167246.2:g.2705874C>T
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_MANN_CTG1	NT_167246.1:g.2711494=	NT_167246.1:g.2711494C>T
LOC101929072 transcript	XM_005275500.1:c.102-2067=	XM_005275500.1:c.102-2067G>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#.

44 SubSNP, 14 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	SC_JCM	ss3516021	Sep 28, 2001 (100)
2	TSC-CSHL	ss5320852	Oct 10, 2002 (110)
3	TSC-CSHL	ss5321623	Oct 10, 2002 (117)
4	GMI	ss156741995	Dec 01, 2009 (137)
5	BCM-HGSC-SUB	ss207787875	Jul 04, 2010 (132)
6	1000GENOMES	ss233397657	Jul 14, 2010 (137)
7	1000GENOMES	ss240468607	Jul 15, 2010 (137)
8	GMI	ss278725397	May 04, 2012 (137)
9	SSMP	ss653033397	Apr 25, 2013 (138)
10	EVA-GONL	ss982763511	Aug 21, 2014 (142)
11	JMKIDD_LAB	ss1073504165	Aug 21, 2014 (142)
12	1000GENOMES	ss1319553220	Aug 21, 2014 (142)
13	HAMMER_LAB	ss1397449629	Sep 08, 2015 (146)
14	WEILL_CORNELL_DGM	ss1926015621	Feb 12, 2016 (147)
15	ILLUMINA	ss1958887663	Feb 12, 2016 (147)
16	USC_VALOUEV	ss2151806750	Dec 20, 2016 (150)
17	GRF	ss2707400304	Nov 08, 2017 (151)
18	ILLUMINA	ss2711069210	Nov 08, 2017 (151)
19	GNOMAD	ss2837414215	Nov 08, 2017 (151)
20	AFFY	ss2985361259	Nov 08, 2017 (151)
21	SWEGEN	ss2998792467	Nov 08, 2017 (151)
22	ILLUMINA	ss3022598905	Nov 08, 2017 (151)
23	BIOINF_KMB_FNS_UNIBA	ss3025607184	Nov 08, 2017 (151)
24	ILLUMINA	ss3653111351	Oct 12, 2018 (152)
25	ILLUMINA	ss3726329727	Jul 13, 2019 (153)
26	ACPOP	ss3733359340	Jul 13, 2019 (153)
27	EVA	ss3764819846	Jul 13, 2019 (153)
28	KHV_HUMAN_GENOMES	ss3807975248	Jul 13, 2019 (153)
29	EVA	ss3829831180	Apr 26, 2020 (154)
30	SGDP_PRJ	ss3864249826	Apr 26, 2020 (154)
31	KRGDB	ss3911024937	Apr 26, 2020 (154)
32	VINODS	ss4025187429	Apr 26, 2021 (155)
33	VINODS	ss4025228561	Apr 26, 2021 (155)
34	TOPMED	ss4698359101	Apr 26, 2021 (155)
35	TOMMO_GENOMICS	ss5176830416	Apr 26, 2021 (155)
36	1000G_HIGH_COVERAGE	ss5267931955	Oct 13, 2022 (156)
37	EVA	ss5364716523	Oct 13, 2022 (156)
38	1000G_HIGH_COVERAGE	ss5553586978	Oct 13, 2022 (156)
39	SANFORD_IMAGENETICS	ss5640086106	Oct 13, 2022 (156)
40	TOMMO_GENOMICS	ss5714683426	Oct 13, 2022 (156)
41	YY_MCH	ss5807304956	Oct 13, 2022 (156)
42	EVA	ss5842023746	Oct 13, 2022 (156)
43	EVA	ss5883239395	Oct 13, 2022 (156)
44	EVA	ss5968588062	Oct 13, 2022 (156)
45	1000Genomes	NC_000006.11 - 31365050	Oct 12, 2018 (152)
46	1000Genomes_30x	NC_000006.12 - 31397273	Oct 13, 2022 (156)
47	Genome-wide autozygosity in Daghestan	NC_000006.10 - 31473029	Apr 26, 2020 (154)
48	gnomAD - Genomes	NC_000006.12 - 31397273	Apr 26, 2021 (155)
49	Genome of the Netherlands Release 5	NC_000006.11 - 31365050	Apr 26, 2020 (154)
50	KOREAN population from KRGDB	NC_000006.11 - 31365050	Apr 26, 2020 (154)
51	Northern Sweden	NC_000006.11 - 31365050	Jul 13, 2019 (153)
52	Qatari	NC_000006.11 - 31365050	Apr 26, 2020 (154)
53	SGDP_PRJ	NC_000006.11 - 31365050	Apr 26, 2020 (154)
54	Siberian	NC_000006.11 - 31365050	Apr 26, 2020 (154)
55	8.3KJPN	NC_000006.11 - 31365050	Apr 26, 2021 (155)
56	14KJPN	NC_000006.12 - 31397273	Oct 13, 2022 (156)
57	TopMed	NC_000006.12 - 31397273	Apr 26, 2021 (155)
58	ALFA	NC_000006.12 - 31397273	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).

Associated ID	History Updated (Build)
rs3997965	Dec 16, 2002 (110)
rs3998322	Aug 27, 2003 (117)
rs76210652	May 04, 2012 (137)
rs115707568	May 04, 2012 (137)
rs117542621	Aug 16, 2010 (132)

Added to this RefSNP Cluster:

Submission IDs	Observation SPDI	Canonical SPDI	Source RSIDs
424281, ss207787875, ss278725397, ss1397449629	NC_000006.10:31473028:C:T	NC_000006.12:31397272:C:T	(self)
31320396, 7762491, 18202331, 6644205, 8057551, 16266806, 4323104, 34799723, ss233397657, ss240468607, ss653033397, ss982763511, ss1073504165, ss1319553220, ss1926015621, ss1958887663, ss2151806750, ss2707400304, ss2711069210, ss2837414215, ss2985361259, ss2998792467, ss3022598905, ss3653111351, ss3733359340, ss3764819846, ss3829831180, ss3864249826, ss3911024937, ss5176830416, ss5364716523, ss5640086106, ss5842023746, ss5968588062	NC_000006.11:31365049:C:T	NC_000006.12:31397272:C:T	(self)
41112913, 221187317, 48520530, 535736659, 12187106184, ss3025607184, ss3726329727, ss3807975248, ss4698359101, ss5267931955, ss5553586978, ss5714683426, ss5807304956, ss5883239395	NC_000006.12:31397272:C:T	NC_000006.12:31397272:C:T	(self)
ss3516021, ss5320852, ss5321623, ss156741995	NT_007592.15:31305049:C:T	NC_000006.12:31397272:C:T	(self)
ss4025187429	NT_113891.3:2877640:C:T	NC_000006.12:31397272:C:T	(self)
ss4025228561	NT_167246.2:2705873:C:T	NC_000006.12:31397272: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 rs2507972

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

rs2507972