Name: rs3212351
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.

rs3212351

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr16:89917680-89917681 (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: delAT
Variation Type: Deletion
Frequency: delAT=0.391601 (103653/264690, TOPMED)
delAT=0.376465 (52666/139896, GnomAD)
AT=0.19205 (5427/28258, 14KJPN) (+ 12 more)
delAT=0.34590 (6406/18520, ALFA)
AT=0.19558 (3278/16760, 8.3KJPN)
delAT=0.4803 (3076/6404, 1000G_30x)
delAT=0.4830 (2419/5008, 1000G)
delAT=0.3317 (1486/4480, Estonian)
delAT=0.3059 (1179/3854, ALSPAC)
delAT=0.3031 (1124/3708, TWINSUK)
AT=0.2369 (434/1832, Korea1K)
delAT=0.316 (315/998, GoNL)
delAT=0.380 (228/600, NorthernSweden)
AT=0.448 (95/212, Vietnamese)
delAT=0.33 (13/40, GENOME_DK)

Clinical Significance: Reported in ClinVar
Gene : Consequence: MC1R : 2KB Upstream Variant
LOC124903759 : Intron Variant
Publications: 1 citation
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: 20231103111315

Population	Group	Sample Size	Ref Allele	Alt Allele	Ref HMOZ	Alt HMOZ	HTRZ	HWEP
Total	Global	18520	AT=0.65410	=0.34590	0.431533	0.123326	0.44514	2
European	Sub	14152	AT=0.68393	=0.31607	0.468344	0.10048	0.431176	0
African	Sub	2898	AT=0.5880	=0.4120	0.342995	0.167012	0.489993	0
African Others	Sub	114	AT=0.535	=0.465	0.245614	0.175439	0.578947	1
African American	Sub	2784	AT=0.5902	=0.4098	0.346983	0.166667	0.486351	0
Asian	Sub	112	AT=0.357	=0.643	0.125	0.410714	0.464286	0
East Asian	Sub	86	AT=0.31	=0.69	0.069767	0.44186	0.488372	0
Other Asian	Sub	26	AT=0.50	=0.50	0.307692	0.307692	0.384615	0
Latin American 1	Sub	146	AT=0.562	=0.438	0.287671	0.164384	0.547945	1
Latin American 2	Sub	610	AT=0.428	=0.572	0.2	0.344262	0.455738	1
South Asian	Sub	98	AT=0.57	=0.43	0.285714	0.142857	0.571429	1
Other	Sub	504	AT=0.579	=0.421	0.325397	0.166667	0.507937	0

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	AT=0.608399	delAT=0.391601
gnomAD - Genomes	Global	Study-wide	139896	AT=0.623535	delAT=0.376465
gnomAD - Genomes	European	Sub	75782	AT=0.67023	delAT=0.32977
gnomAD - Genomes	African	Sub	41904	AT=0.58574	delAT=0.41426
gnomAD - Genomes	American	Sub	13638	AT=0.52618	delAT=0.47382
gnomAD - Genomes	Ashkenazi Jewish	Sub	3318	AT=0.6781	delAT=0.3219
gnomAD - Genomes	East Asian	Sub	3102	AT=0.3785	delAT=0.6215
gnomAD - Genomes	Other	Sub	2152	AT=0.6013	delAT=0.3987
14KJPN	JAPANESE	Study-wide	28258	AT=0.19205	delAT=0.80795
Allele Frequency Aggregator	Total	Global	18520	AT=0.65410	delAT=0.34590
Allele Frequency Aggregator	European	Sub	14152	AT=0.68393	delAT=0.31607
Allele Frequency Aggregator	African	Sub	2898	AT=0.5880	delAT=0.4120
Allele Frequency Aggregator	Latin American 2	Sub	610	AT=0.428	delAT=0.572
Allele Frequency Aggregator	Other	Sub	504	AT=0.579	delAT=0.421
Allele Frequency Aggregator	Latin American 1	Sub	146	AT=0.562	delAT=0.438
Allele Frequency Aggregator	Asian	Sub	112	AT=0.357	delAT=0.643
Allele Frequency Aggregator	South Asian	Sub	98	AT=0.57	delAT=0.43
8.3KJPN	JAPANESE	Study-wide	16760	AT=0.19558	delAT=0.80442
1000Genomes_30x	Global	Study-wide	6404	AT=0.5197	delAT=0.4803
1000Genomes_30x	African	Sub	1786	AT=0.5622	delAT=0.4378
1000Genomes_30x	Europe	Sub	1266	AT=0.6627	delAT=0.3373
1000Genomes_30x	South Asian	Sub	1202	AT=0.4900	delAT=0.5100
1000Genomes_30x	East Asian	Sub	1170	AT=0.3786	delAT=0.6214
1000Genomes_30x	American	Sub	980	AT=0.462	delAT=0.538
1000Genomes	Global	Study-wide	5008	AT=0.5170	delAT=0.4830
1000Genomes	African	Sub	1322	AT=0.5598	delAT=0.4402
1000Genomes	East Asian	Sub	1008	AT=0.3720	delAT=0.6280
1000Genomes	Europe	Sub	1006	AT=0.6680	delAT=0.3320
1000Genomes	South Asian	Sub	978	AT=0.501	delAT=0.499
1000Genomes	American	Sub	694	AT=0.450	delAT=0.550
Genetic variation in the Estonian population	Estonian	Study-wide	4480	AT=0.6683	delAT=0.3317
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	AT=0.6941	delAT=0.3059
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	AT=0.6969	delAT=0.3031
Korean Genome Project	KOREAN	Study-wide	1832	AT=0.2369	delAT=0.7631
Genome of the Netherlands Release 5	Genome of the Netherlands	Study-wide	998	AT=0.684	delAT=0.316
Northern Sweden	ACPOP	Study-wide	600	AT=0.620	delAT=0.380
A Vietnamese Genetic Variation Database	Global	Study-wide	212	AT=0.448	delAT=0.552
The Danish reference pan genome	Danish	Study-wide	40	AT=0.68	delAT=0.33

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 16	NC_000016.10:g.89917680_89917681del
GRCh37.p13 chr 16	NC_000016.9:g.89984088_89984089del
TUBB3 RefSeqGene	NG_027810.1:g.672_673del
MC1R RefSeqGene	NG_012026.1:g.4802_4803del

Gene: MC1R, melanocortin 1 receptor (plus strand) : 2KB Upstream Variant

Molecule type	Change	Amino acid[Codon]	SO Term
MC1R transcript	NM_002386.4:c.	N/A	Upstream Transcript Variant

Gene: LOC124903759, uncharacterized LOC124903759 (plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
LOC124903759 transcript variant X1	XM_047435031.1:c.1041-196… XM_047435031.1:c.1041-196_1041-195del	N/A	Intron Variant
LOC124903759 transcript variant X2	XM_047435032.1:c.1041-147… XM_047435032.1:c.1041-147_1041-146del	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.

Allele: delAT (allele ID: 1255336 )

ClinVar Accession	Disease Names	Clinical Significance
RCV001677783.2	not provided	Benign

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	AT=	delAT
GRCh38.p14 chr 16	NC_000016.10:g.89917680_89917681=	NC_000016.10:g.89917680_89917681del
GRCh37.p13 chr 16	NC_000016.9:g.89984088_89984089=	NC_000016.9:g.89984088_89984089del
TUBB3 RefSeqGene	NG_027810.1:g.672_673=	NG_027810.1:g.672_673del
MC1R RefSeqGene	NG_012026.1:g.4802_4803=	NG_012026.1:g.4802_4803del
LOC124903759 transcript variant X1	XM_047435031.1:c.1041-196=	XM_047435031.1:c.1041-196_1041-195del
LOC124903759 transcript variant X2	XM_047435032.1:c.1041-147=	XM_047435032.1:c.1041-147_1041-146del

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#.

61 SubSNP, 15 Frequency, 1 ClinVar submissions

No	Submitter	Submission ID	Date (Build)
1	PGA-UW-FHCRC	ss4472723	Jul 03, 2002 (106)
2	DEVINE_LAB	ss14952987	Mar 15, 2016 (147)
3	HGSV	ss79754468	Dec 15, 2007 (130)
4	HGSV	ss81546564	Dec 15, 2007 (130)
5	HGSV	ss81757402	Dec 15, 2007 (130)
6	GMI	ss155683006	Dec 01, 2009 (131)
7	GMI	ss288483590	May 09, 2011 (134)
8	GMI	ss289310539	May 04, 2012 (137)
9	PJP	ss294900705	May 09, 2011 (135)
10	1000GENOMES	ss327760753	May 09, 2011 (135)
11	1000GENOMES	ss327883971	May 09, 2011 (135)
12	1000GENOMES	ss328207603	May 09, 2011 (135)
13	1000GENOMES	ss499170921	May 04, 2012 (137)
14	ILLUMINA	ss537168143	Sep 08, 2015 (146)
15	LUNTER	ss552501201	Apr 25, 2013 (138)
16	TISHKOFF	ss554846091	Apr 25, 2013 (138)
17	SSMP	ss664340117	Apr 01, 2015 (144)
18	BILGI_BIOE	ss666681090	Apr 25, 2013 (138)
19	ILLUMINA	ss778703443	Aug 21, 2014 (144)
20	ILLUMINA	ss834162467	Aug 21, 2014 (144)
21	EVA-GONL	ss992830702	Aug 21, 2014 (142)
22	1000GENOMES	ss1376259353	Aug 21, 2014 (142)
23	EVA_GENOME_DK	ss1575006533	Apr 01, 2015 (144)
24	EVA_DECODE	ss1696872278	Apr 01, 2015 (144)
25	EVA_UK10K_ALSPAC	ss1708651241	Apr 01, 2015 (144)
26	EVA_UK10K_TWINSUK	ss1708651275	Apr 01, 2015 (144)
27	HAMMER_LAB	ss1808662910	Sep 08, 2015 (146)
28	GENOMED	ss1968333620	Jul 19, 2016 (147)
29	JJLAB	ss2031320798	Sep 14, 2016 (149)
30	SYSTEMSBIOZJU	ss2628953367	Nov 08, 2017 (151)
31	ILLUMINA	ss2633363324	Nov 08, 2017 (151)
32	SWEGEN	ss3015041354	Nov 08, 2017 (151)
33	MCHAISSO	ss3064697633	Nov 08, 2017 (151)
34	ILLUMINA	ss3627602916	Oct 12, 2018 (152)
35	ILLUMINA	ss3631346717	Oct 12, 2018 (152)
36	BEROUKHIMLAB	ss3644406492	Oct 12, 2018 (152)
37	BIOINF_KMB_FNS_UNIBA	ss3645435731	Oct 12, 2018 (152)
38	EGCUT_WGS	ss3682019150	Jul 13, 2019 (153)
39	EVA_DECODE	ss3699905701	Jul 13, 2019 (153)
40	ACPOP	ss3741791938	Jul 13, 2019 (153)
41	PACBIO	ss3788124128	Jul 13, 2019 (153)
42	PACBIO	ss3793095023	Jul 13, 2019 (153)
43	PACBIO	ss3797980425	Jul 13, 2019 (153)
44	KHV_HUMAN_GENOMES	ss3819613381	Jul 13, 2019 (153)
45	EVA	ss3834732204	Apr 27, 2020 (154)
46	EVA	ss3840973429	Apr 27, 2020 (154)
47	EVA	ss3846467172	Apr 27, 2020 (154)
48	KOGIC	ss3978222898	Apr 27, 2020 (154)
49	GNOMAD	ss4306492589	Apr 27, 2021 (155)
50	TOPMED	ss5026621879	Apr 27, 2021 (155)
51	TOMMO_GENOMICS	ss5221066969	Apr 27, 2021 (155)
52	1000G_HIGH_COVERAGE	ss5302107283	Oct 16, 2022 (156)
53	HUGCELL_USP	ss5495328236	Oct 16, 2022 (156)
54	1000G_HIGH_COVERAGE	ss5605329257	Oct 16, 2022 (156)
55	SANFORD_IMAGENETICS	ss5659545386	Oct 16, 2022 (156)
56	TOMMO_GENOMICS	ss5776520142	Oct 16, 2022 (156)
57	YY_MCH	ss5816253010	Oct 16, 2022 (156)
58	EVA	ss5846860219	Oct 16, 2022 (156)
59	EVA	ss5851702263	Oct 16, 2022 (156)
60	EVA	ss5900402785	Oct 16, 2022 (156)
61	EVA	ss5950960188	Oct 16, 2022 (156)
62	1000Genomes	NC_000016.9 - 89984088	Oct 12, 2018 (152)
63	1000Genomes_30x	NC_000016.10 - 89917680	Oct 16, 2022 (156)
64	The Avon Longitudinal Study of Parents and Children	NC_000016.9 - 89984088	Oct 12, 2018 (152)
65	Genetic variation in the Estonian population	NC_000016.9 - 89984088	Oct 12, 2018 (152)
66	The Danish reference pan genome	NC_000016.9 - 89984088	Apr 27, 2020 (154)
67	gnomAD - Genomes	NC_000016.10 - 89917680	Apr 27, 2021 (155)
68	Genome of the Netherlands Release 5	NC_000016.9 - 89984088	Apr 27, 2020 (154)
69	Korean Genome Project	NC_000016.10 - 89917680	Apr 27, 2020 (154)
70	Northern Sweden	NC_000016.9 - 89984088	Jul 13, 2019 (153)
71	8.3KJPN	NC_000016.9 - 89984088	Apr 27, 2021 (155)
72	14KJPN	NC_000016.10 - 89917680	Oct 16, 2022 (156)
73	TopMed	NC_000016.10 - 89917680	Apr 27, 2021 (155)
74	UK 10K study - Twins	NC_000016.9 - 89984088	Oct 12, 2018 (152)
75	A Vietnamese Genetic Variation Database	NC_000016.9 - 89984088	Jul 13, 2019 (153)
76	ALFA	NC_000016.10 - 89917680	Apr 27, 2021 (155)
77	ClinVar	RCV001677783.2	Oct 16, 2022 (156)

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)
rs35269804	May 23, 2006 (127)
rs58769746	May 24, 2008 (130)
rs139125587	Sep 17, 2011 (135)
rs145423070	Sep 17, 2011 (135)
rs386580895	Apr 01, 2015 (144)

Added to this RefSNP Cluster:

Submission IDs	Observation SPDI	Canonical SPDI	Source RSIDs
ss79754468, ss81546564, ss81757402, ss289310539, ss294900705, ss327760753, ss327883971, ss328207603, ss552501201, ss1696872278	NC_000016.8:88511588:AT:	NC_000016.10:89917679:AT:	(self)
70762722, 39253456, 27757398, 544733, 17497950, 15076803, 79036276, 39253456, 8697211, ss499170921, ss537168143, ss554846091, ss664340117, ss666681090, ss778703443, ss834162467, ss992830702, ss1376259353, ss1575006533, ss1708651241, ss1708651275, ss1808662910, ss1968333620, ss2031320798, ss2628953367, ss2633363324, ss3015041354, ss3627602916, ss3631346717, ss3644406492, ss3682019150, ss3741791938, ss3788124128, ss3793095023, ss3797980425, ss3834732204, ss3840973429, ss5221066969, ss5659545386, ss5846860219, ss5950960188	NC_000016.9:89984087:AT:	NC_000016.10:89917679:AT:	(self)
RCV001677783.2, 92855192, 498996680, 34600899, 110357246, 242167540, 4916891628, ss3064697633, ss3645435731, ss3699905701, ss3819613381, ss3846467172, ss3978222898, ss4306492589, ss5026621879, ss5302107283, ss5495328236, ss5605329257, ss5776520142, ss5816253010, ss5851702263, ss5900402785	NC_000016.10:89917679:AT:	NC_000016.10:89917679:AT:	(self)
ss4472723, ss14952987, ss155683006, ss288483590	NT_010542.15:1544704:AT:	NC_000016.10:89917679:AT:	(self)

Publications tab displays PubMed articles citing the variation as a listing of PMID, Title, Author, Year, Journal, ordered by Year, descending.

1 citation for rs3212351

PMID	Title	Author	Year	Journal
20158590	Predicting phenotype from genotype: normal pigmentation.	Valenzuela RK et al.	2010	Journal of forensic sciences

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

rs3212351