Name: rs76418398
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.

rs76418398

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr3:151294467 (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: A>C
Variation Type: SNV Single Nucleotide Variation
Frequency: C=0.000006 (1/164676, ALFA)
C=0.022559 (2709/120086, ExAC)
C=0.00007 (2/28258, 14KJPN) (+ 2 more)
C=0.00018 (3/16760, 8.3KJPN)
C=0.0147 (27/1832, Korea1K)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: GPR87 : Missense Variant
MED12L : 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	164796	A=0.999994	C=0.000006
European	Sub	147514	A=0.999993	C=0.000007
African	Sub	1142	A=1.0000	C=0.0000
African Others	Sub	64	A=1.00	C=0.00
African American	Sub	1078	A=1.0000	C=0.0000
Asian	Sub	6158	A=1.0000	C=0.0000
East Asian	Sub	4366	A=1.0000	C=0.0000
Other Asian	Sub	1792	A=1.0000	C=0.0000
Latin American 1	Sub	306	A=1.000	C=0.000
Latin American 2	Sub	408	A=1.000	C=0.000
South Asian	Sub	192	A=1.000	C=0.000
Other	Sub	9076	A=1.0000	C=0.0000

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
Allele Frequency Aggregator	Total	Global	164676	A=0.999994	C=0.000006
Allele Frequency Aggregator	European	Sub	147412	A=0.999993	C=0.000007
Allele Frequency Aggregator	Other	Sub	9072	A=1.0000	C=0.0000
Allele Frequency Aggregator	Asian	Sub	6158	A=1.0000	C=0.0000
Allele Frequency Aggregator	African	Sub	1128	A=1.0000	C=0.0000
Allele Frequency Aggregator	Latin American 2	Sub	408	A=1.000	C=0.000
Allele Frequency Aggregator	Latin American 1	Sub	306	A=1.000	C=0.000
Allele Frequency Aggregator	South Asian	Sub	192	A=1.000	C=0.000
ExAC	Global	Study-wide	120086	A=0.977441	C=0.022559
ExAC	Europe	Sub	72476	A=0.97016	C=0.02984
ExAC	Asian	Sub	25096	A=0.99681	C=0.00319
ExAC	American	Sub	11518	A=0.99358	C=0.00642
ExAC	African	Sub	10090	A=0.96551	C=0.03449
ExAC	Other	Sub	906	A=0.951	C=0.049
14KJPN	JAPANESE	Study-wide	28258	A=0.99993	C=0.00007
8.3KJPN	JAPANESE	Study-wide	16760	A=0.99982	C=0.00018
Korean Genome Project	KOREAN	Study-wide	1832	A=0.9853	C=0.0147

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 3	NC_000003.12:g.151294467A>C
GRCh37.p13 chr 3	NC_000003.11:g.151012255A>C
MED12L RefSeqGene	NG_021244.1:g.212580A>C

Gene: MED12L, mediator complex subunit 12L (plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
MED12L transcript variant 1	NM_001393769.1:c.2251-555… NM_001393769.1:c.2251-55592A>C	N/A	Intron Variant
MED12L transcript variant 2	NM_053002.6:c.2146-55592A… NM_053002.6:c.2146-55592A>C	N/A	Intron Variant
MED12L transcript variant X20	XM_011512394.3:c.2251-555… XM_011512394.3:c.2251-55592A>C	N/A	Intron Variant
MED12L transcript variant X22	XM_011512399.4:c.2251-555… XM_011512399.4:c.2251-55592A>C	N/A	Intron Variant
MED12L transcript variant X1	XM_017005676.2:c.2251-555… XM_017005676.2:c.2251-55592A>C	N/A	Intron Variant
MED12L transcript variant X3	XM_017005677.2:c.2251-555… XM_017005677.2:c.2251-55592A>C	N/A	Intron Variant
MED12L transcript variant X6	XM_017005678.2:c.2251-555… XM_017005678.2:c.2251-55592A>C	N/A	Intron Variant
MED12L transcript variant X12	XM_017005679.2:c.1981-555… XM_017005679.2:c.1981-55592A>C	N/A	Intron Variant
MED12L transcript variant X14	XM_017005680.2:c.1969-555… XM_017005680.2:c.1969-55592A>C	N/A	Intron Variant
MED12L transcript variant X2	XM_047447403.1:c.2251-555… XM_047447403.1:c.2251-55592A>C	N/A	Intron Variant
MED12L transcript variant X4	XM_047447404.1:c.2251-555… XM_047447404.1:c.2251-55592A>C	N/A	Intron Variant
MED12L transcript variant X5	XM_047447405.1:c.2251-555… XM_047447405.1:c.2251-55592A>C	N/A	Intron Variant
MED12L transcript variant X7	XM_047447406.1:c.2251-555… XM_047447406.1:c.2251-55592A>C	N/A	Intron Variant
MED12L transcript variant X8	XM_047447407.1:c.2146-555… XM_047447407.1:c.2146-55592A>C	N/A	Intron Variant
MED12L transcript variant X9	XM_047447408.1:c.2146-555… XM_047447408.1:c.2146-55592A>C	N/A	Intron Variant
MED12L transcript variant X10	XM_047447409.1:c.2146-555… XM_047447409.1:c.2146-55592A>C	N/A	Intron Variant
MED12L transcript variant X11	XM_047447410.1:c.2146-555… XM_047447410.1:c.2146-55592A>C	N/A	Intron Variant
MED12L transcript variant X13	XM_047447411.1:c.1981-555… XM_047447411.1:c.1981-55592A>C	N/A	Intron Variant
MED12L transcript variant X15	XM_047447412.1:c.1969-555… XM_047447412.1:c.1969-55592A>C	N/A	Intron Variant
MED12L transcript variant X16	XM_047447413.1:c.1969-555… XM_047447413.1:c.1969-55592A>C	N/A	Intron Variant
MED12L transcript variant X17	XM_047447414.1:c.1969-555… XM_047447414.1:c.1969-55592A>C	N/A	Intron Variant
MED12L transcript variant X18	XM_047447416.1:c.1969-555… XM_047447416.1:c.1969-55592A>C	N/A	Intron Variant
MED12L transcript variant X19	XM_047447417.1:c.1876-555… XM_047447417.1:c.1876-55592A>C	N/A	Intron Variant
MED12L transcript variant X21	XM_047447418.1:c.2251-555… XM_047447418.1:c.2251-55592A>C	N/A	Intron Variant

Gene: GPR87, G protein-coupled receptor 87 (minus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
GPR87 transcript	NM_023915.4:c.779T>G	V [GTG] > G [GGG]	Coding Sequence Variant
G-protein coupled receptor 87	NP_076404.3:p.Val260Gly	V (Val) > G (Gly)	Missense 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	A=	C
GRCh38.p14 chr 3	NC_000003.12:g.151294467=	NC_000003.12:g.151294467A>C
GRCh37.p13 chr 3	NC_000003.11:g.151012255=	NC_000003.11:g.151012255A>C
MED12L RefSeqGene	NG_021244.1:g.212580=	NG_021244.1:g.212580A>C
GPR87 transcript	NM_023915.4:c.779=	NM_023915.4:c.779T>G
GPR87 transcript	NM_023915.3:c.779=	NM_023915.3:c.779T>G
G-protein coupled receptor 87	NP_076404.3:p.Val260=	NP_076404.3:p.Val260Gly
MED12L transcript variant 1	NM_001393769.1:c.2251-55592=	NM_001393769.1:c.2251-55592A>C
MED12L transcript	NM_053002.4:c.2146-55592=	NM_053002.4:c.2146-55592A>C
MED12L transcript variant 2	NM_053002.6:c.2146-55592=	NM_053002.6:c.2146-55592A>C
MED12L transcript variant X1	XM_005247096.1:c.2251-55592=	XM_005247096.1:c.2251-55592A>C
MED12L transcript variant X20	XM_011512394.3:c.2251-55592=	XM_011512394.3:c.2251-55592A>C
MED12L transcript variant X22	XM_011512399.4:c.2251-55592=	XM_011512399.4:c.2251-55592A>C
MED12L transcript variant X1	XM_017005676.2:c.2251-55592=	XM_017005676.2:c.2251-55592A>C
MED12L transcript variant X3	XM_017005677.2:c.2251-55592=	XM_017005677.2:c.2251-55592A>C
MED12L transcript variant X6	XM_017005678.2:c.2251-55592=	XM_017005678.2:c.2251-55592A>C
MED12L transcript variant X12	XM_017005679.2:c.1981-55592=	XM_017005679.2:c.1981-55592A>C
MED12L transcript variant X14	XM_017005680.2:c.1969-55592=	XM_017005680.2:c.1969-55592A>C
MED12L transcript variant X2	XM_047447403.1:c.2251-55592=	XM_047447403.1:c.2251-55592A>C
MED12L transcript variant X4	XM_047447404.1:c.2251-55592=	XM_047447404.1:c.2251-55592A>C
MED12L transcript variant X5	XM_047447405.1:c.2251-55592=	XM_047447405.1:c.2251-55592A>C
MED12L transcript variant X7	XM_047447406.1:c.2251-55592=	XM_047447406.1:c.2251-55592A>C
MED12L transcript variant X8	XM_047447407.1:c.2146-55592=	XM_047447407.1:c.2146-55592A>C
MED12L transcript variant X9	XM_047447408.1:c.2146-55592=	XM_047447408.1:c.2146-55592A>C
MED12L transcript variant X10	XM_047447409.1:c.2146-55592=	XM_047447409.1:c.2146-55592A>C
MED12L transcript variant X11	XM_047447410.1:c.2146-55592=	XM_047447410.1:c.2146-55592A>C
MED12L transcript variant X13	XM_047447411.1:c.1981-55592=	XM_047447411.1:c.1981-55592A>C
MED12L transcript variant X15	XM_047447412.1:c.1969-55592=	XM_047447412.1:c.1969-55592A>C
MED12L transcript variant X16	XM_047447413.1:c.1969-55592=	XM_047447413.1:c.1969-55592A>C
MED12L transcript variant X17	XM_047447414.1:c.1969-55592=	XM_047447414.1:c.1969-55592A>C
MED12L transcript variant X18	XM_047447416.1:c.1969-55592=	XM_047447416.1:c.1969-55592A>C
MED12L transcript variant X19	XM_047447417.1:c.1876-55592=	XM_047447417.1:c.1876-55592A>C
MED12L transcript variant X21	XM_047447418.1:c.2251-55592=	XM_047447418.1:c.2251-55592A>C

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#.

37 SubSNP, 5 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	ILLUMINA	ss161078466	Dec 01, 2009 (131)
2	ILLUMINA	ss479456736	Sep 08, 2015 (146)
3	ILLUMINA	ss484233051	May 04, 2012 (137)
4	ILLUMINA	ss484485849	May 04, 2012 (137)
5	EXOME_CHIP	ss491347852	May 04, 2012 (137)
6	CLINSEQ_SNP	ss491844176	May 04, 2012 (137)
7	ILLUMINA	ss779153262	Sep 08, 2015 (146)
8	ILLUMINA	ss780823217	Sep 08, 2015 (146)
9	ILLUMINA	ss782562503	Sep 08, 2015 (146)
10	ILLUMINA	ss783505744	Sep 08, 2015 (146)
11	ILLUMINA	ss834618166	Sep 08, 2015 (146)
12	EVA_EXAC	ss1687259843	Apr 01, 2015 (144)
13	ILLUMINA	ss1752446871	Sep 08, 2015 (146)
14	ILLUMINA	ss1917774117	Feb 12, 2016 (147)
15	ILLUMINA	ss1946099428	Feb 12, 2016 (147)
16	ILLUMINA	ss1958618411	Feb 12, 2016 (147)
17	ILLUMINA	ss2634028935	Nov 08, 2017 (151)
18	GRF	ss2705346853	Nov 08, 2017 (151)
19	GNOMAD	ss2734147619	Nov 08, 2017 (151)
20	AFFY	ss2985273814	Nov 08, 2017 (151)
21	ILLUMINA	ss3628807303	Oct 12, 2018 (152)
22	ILLUMINA	ss3631970902	Oct 12, 2018 (152)
23	ILLUMINA	ss3634923415	Oct 12, 2018 (152)
24	ILLUMINA	ss3636620810	Oct 12, 2018 (152)
25	ILLUMINA	ss3640630713	Oct 12, 2018 (152)
26	ILLUMINA	ss3644832084	Oct 12, 2018 (152)
27	ILLUMINA	ss3654043360	Oct 12, 2018 (152)
28	ILLUMINA	ss3744517570	Jul 13, 2019 (153)
29	ILLUMINA	ss3745223388	Jul 13, 2019 (153)
30	ILLUMINA	ss3772718579	Jul 13, 2019 (153)
31	KOGIC	ss3952682795	Apr 25, 2020 (154)
32	EVA	ss3986025118	Apr 26, 2021 (155)
33	TOMMO_GENOMICS	ss5162210408	Apr 26, 2021 (155)
34	EVA	ss5344161119	Oct 17, 2022 (156)
35	TOMMO_GENOMICS	ss5695269857	Oct 17, 2022 (156)
36	EVA	ss5847986602	Oct 17, 2022 (156)
37	EVA	ss5961828490	Oct 17, 2022 (156)
38	ExAC	NC_000003.11 - 151012255	Oct 12, 2018 (152)
39	Korean Genome Project	NC_000003.12 - 151294467	Apr 25, 2020 (154)
40	8.3KJPN	NC_000003.11 - 151012255	Apr 26, 2021 (155)
41	14KJPN	NC_000003.12 - 151294467	Oct 17, 2022 (156)
42	ALFA	NC_000003.12 - 151294467	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).

Added to this RefSNP Cluster:

Submission IDs	Observation SPDI	Canonical SPDI	Source RSIDs
ss484485849, ss491844176	NC_000003.10:152494944:A:C	NC_000003.12:151294466:A:C	(self)
7203487, 20179715, ss479456736, ss484233051, ss491347852, ss779153262, ss780823217, ss782562503, ss783505744, ss834618166, ss1687259843, ss1752446871, ss1917774117, ss1946099428, ss1958618411, ss2634028935, ss2705346853, ss2734147619, ss2985273814, ss3628807303, ss3631970902, ss3634923415, ss3636620810, ss3640630713, ss3644832084, ss3654043360, ss3744517570, ss3745223388, ss3772718579, ss3986025118, ss5162210408, ss5344161119, ss5847986602, ss5961828490	NC_000003.11:151012254:A:C	NC_000003.12:151294466:A:C	(self)
9060796, 29106961, 5760797689, ss3952682795, ss5695269857	NC_000003.12:151294466:A:C	NC_000003.12:151294466:A:C	(self)
ss161078466	NT_005612.16:57507400:A:C	NC_000003.12:151294466:A:C	(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 rs76418398

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

rs76418398