Name: rs111383277
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.

rs111383277

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr17:41612568 (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: G>A / G>C / G>T
Variation Type: SNV Single Nucleotide Variation
Frequency: A=0.013843 (3664/264690, TOPMED)
A=0.015977 (2241/140260, GnomAD)
A=0.02384 (1372/57548, ExAC) (+ 12 more)
A=0.01675 (546/32590, ALFA)
A=0.01718 (221/12864, GO-ESP)
A=0.0078 (50/6404, 1000G_30x)
A=0.0070 (35/5008, 1000G)
A=0.0267 (103/3854, ALSPAC)
A=0.0232 (86/3708, TWINSUK)
A=0.039 (39/998, GoNL)
A=0.025 (15/600, NorthernSweden)
A=0.006 (3/534, MGP)
G=0.2 (1/4, SGDP_PRJ)
G=0.5 (2/4, Siberian)
A=0.5 (2/4, Siberian)

Clinical Significance: Reported in ClinVar
Gene : Consequence: KRT16 : Missense 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	32612	G=0.98323	A=0.01677
European	Sub	24892	G=0.98084	A=0.01916
African	Sub	3540	G=0.9955	A=0.0045
African Others	Sub	122	G=1.000	A=0.000
African American	Sub	3418	G=0.9953	A=0.0047
Asian	Sub	168	G=1.000	A=0.000
East Asian	Sub	112	G=1.000	A=0.000
Other Asian	Sub	56	G=1.00	A=0.00
Latin American 1	Sub	146	G=0.973	A=0.027
Latin American 2	Sub	610	G=0.993	A=0.007
South Asian	Sub	98	G=1.00	A=0.00
Other	Sub	3158	G=0.9854	A=0.0146

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	G=0.986157	A=0.013843
gnomAD - Genomes	Global	Study-wide	140260	G=0.984023	A=0.015977
gnomAD - Genomes	European	Sub	75944	G=0.97505	A=0.02495
gnomAD - Genomes	African	Sub	42040	G=0.99508	A=0.00492
gnomAD - Genomes	American	Sub	13664	G=0.99305	A=0.00695
gnomAD - Genomes	Ashkenazi Jewish	Sub	3324	G=0.9967	A=0.0033
gnomAD - Genomes	East Asian	Sub	3134	G=1.0000	A=0.0000
gnomAD - Genomes	Other	Sub	2154	G=0.9847	A=0.0153
ExAC	Global	Study-wide	57548	G=0.97616	A=0.02384
ExAC	Europe	Sub	33490	G=0.96494	A=0.03506
ExAC	Asian	Sub	15066	G=0.99223	A=0.00777
ExAC	African	Sub	4612	G=0.9939	A=0.0061
ExAC	American	Sub	3862	G=0.9894	A=0.0106
ExAC	Other	Sub	518	G=0.977	A=0.023
Allele Frequency Aggregator	Total	Global	32590	G=0.98325	A=0.01675
Allele Frequency Aggregator	European	Sub	24874	G=0.98086	A=0.01914
Allele Frequency Aggregator	African	Sub	3540	G=0.9955	A=0.0045
Allele Frequency Aggregator	Other	Sub	3154	G=0.9854	A=0.0146
Allele Frequency Aggregator	Latin American 2	Sub	610	G=0.993	A=0.007
Allele Frequency Aggregator	Asian	Sub	168	G=1.000	A=0.000
Allele Frequency Aggregator	Latin American 1	Sub	146	G=0.973	A=0.027
Allele Frequency Aggregator	South Asian	Sub	98	G=1.00	A=0.00
GO Exome Sequencing Project	Global	Study-wide	12864	G=0.98282	A=0.01718
GO Exome Sequencing Project	European American	Sub	8510	G=0.9756	A=0.0244
GO Exome Sequencing Project	African American	Sub	4354	G=0.9970	A=0.0030
1000Genomes_30x	Global	Study-wide	6404	G=0.9922	A=0.0078
1000Genomes_30x	African	Sub	1786	G=0.9983	A=0.0017
1000Genomes_30x	Europe	Sub	1266	G=0.9771	A=0.0229
1000Genomes_30x	South Asian	Sub	1202	G=0.9917	A=0.0083
1000Genomes_30x	East Asian	Sub	1170	G=1.0000	A=0.0000
1000Genomes_30x	American	Sub	980	G=0.992	A=0.008
1000Genomes	Global	Study-wide	5008	G=0.9930	A=0.0070
1000Genomes	African	Sub	1322	G=0.9985	A=0.0015
1000Genomes	East Asian	Sub	1008	G=1.0000	A=0.0000
1000Genomes	Europe	Sub	1006	G=0.9801	A=0.0199
1000Genomes	South Asian	Sub	978	G=0.993	A=0.007
1000Genomes	American	Sub	694	G=0.991	A=0.009
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	G=0.9733	A=0.0267
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	G=0.9768	A=0.0232
Genome of the Netherlands Release 5	Genome of the Netherlands	Study-wide	998	G=0.961	A=0.039
Northern Sweden	ACPOP	Study-wide	600	G=0.975	A=0.025
Medical Genome Project healthy controls from Spanish population	Spanish controls	Study-wide	534	G=0.994	A=0.006
SGDP_PRJ	Global	Study-wide	4	G=0.2	A=0.8
Siberian	Global	Study-wide	4	G=0.5	A=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 17	NC_000017.11:g.41612568G>A
GRCh38.p14 chr 17	NC_000017.11:g.41612568G>C
GRCh38.p14 chr 17	NC_000017.11:g.41612568G>T
GRCh37.p13 chr 17	NC_000017.10:g.39768820G>A
GRCh37.p13 chr 17	NC_000017.10:g.39768820G>C
GRCh37.p13 chr 17	NC_000017.10:g.39768820G>T
KRT16 RefSeqGene	NG_008301.1:g.5260C>T
KRT16 RefSeqGene	NG_008301.1:g.5260C>G
KRT16 RefSeqGene	NG_008301.1:g.5260C>A

Gene: KRT16, keratin 16 (minus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
KRT16 transcript	NM_005557.4:c.121C>T	R [CGT] > C [TGT]	Coding Sequence Variant
keratin, type I cytoskeletal 16	NP_005548.2:p.Arg41Cys	R (Arg) > C (Cys)	Missense Variant
KRT16 transcript	NM_005557.4:c.121C>G	R [CGT] > G [GGT]	Coding Sequence Variant
keratin, type I cytoskeletal 16	NP_005548.2:p.Arg41Gly	R (Arg) > G (Gly)	Missense Variant
KRT16 transcript	NM_005557.4:c.121C>A	R [CGT] > S [AGT]	Coding Sequence Variant
keratin, type I cytoskeletal 16	NP_005548.2:p.Arg41Ser	R (Arg) > S (Ser)	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.

Allele: A (allele ID: 1662219 )

ClinVar Accession	Disease Names	Clinical Significance
RCV002132110.3	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	G=	A	C	T
GRCh38.p14 chr 17	NC_000017.11:g.41612568=	NC_000017.11:g.41612568G>A	NC_000017.11:g.41612568G>C	NC_000017.11:g.41612568G>T
GRCh37.p13 chr 17	NC_000017.10:g.39768820=	NC_000017.10:g.39768820G>A	NC_000017.10:g.39768820G>C	NC_000017.10:g.39768820G>T
KRT16 RefSeqGene	NG_008301.1:g.5260=	NG_008301.1:g.5260C>T	NG_008301.1:g.5260C>G	NG_008301.1:g.5260C>A
KRT16 transcript	NM_005557.4:c.121=	NM_005557.4:c.121C>T	NM_005557.4:c.121C>G	NM_005557.4:c.121C>A
KRT16 transcript	NM_005557.3:c.121=	NM_005557.3:c.121C>T	NM_005557.3:c.121C>G	NM_005557.3:c.121C>A
keratin, type I cytoskeletal 16	NP_005548.2:p.Arg41=	NP_005548.2:p.Arg41Cys	NP_005548.2:p.Arg41Gly	NP_005548.2:p.Arg41Ser

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#.

43 SubSNP, 16 Frequency, 1 ClinVar submissions

No	Submitter	Submission ID	Date (Build)
1	COMPLETE_GENOMICS	ss168146232	Jul 04, 2010 (132)
2	BL	ss255635119	May 09, 2011 (134)
3	1000GENOMES	ss339693262	May 09, 2011 (134)
4	EXOME_CHIP	ss491522429	May 04, 2012 (137)
5	CLINSEQ_SNP	ss491736580	May 04, 2012 (137)
6	ILLUMINA	ss536516043	Sep 08, 2015 (146)
7	NHLBI-ESP	ss713384085	Apr 25, 2013 (138)
8	EVA-GONL	ss993103370	Aug 21, 2014 (142)
9	1000GENOMES	ss1358633856	Aug 21, 2014 (142)
10	EVA_UK10K_ALSPAC	ss1635642899	Apr 01, 2015 (144)
11	EVA_UK10K_TWINSUK	ss1678636932	Apr 01, 2015 (144)
12	EVA_EXAC	ss1692776069	Apr 01, 2015 (144)
13	EVA_DECODE	ss1697145741	Apr 01, 2015 (144)
14	EVA_MGP	ss1711460708	Apr 01, 2015 (144)
15	JJLAB	ss2029059417	Sep 14, 2016 (149)
16	USC_VALOUEV	ss2157528498	Dec 20, 2016 (150)
17	GNOMAD	ss2742712175	Nov 08, 2017 (151)
18	GNOMAD	ss2749773369	Nov 08, 2017 (151)
19	GNOMAD	ss2949801718	Nov 08, 2017 (151)
20	AFFY	ss2985095326	Nov 08, 2017 (151)
21	SWEGEN	ss3015524816	Nov 08, 2017 (151)
22	CSHL	ss3351744822	Nov 08, 2017 (151)
23	ILLUMINA	ss3627668343	Oct 12, 2018 (152)
24	ILLUMINA	ss3653867131	Oct 12, 2018 (152)
25	EVA_DECODE	ss3700455167	Jul 13, 2019 (153)
26	ACPOP	ss3742022357	Jul 13, 2019 (153)
27	KHV_HUMAN_GENOMES	ss3819931558	Jul 13, 2019 (153)
28	EVA	ss3825113406	Apr 27, 2020 (154)
29	EVA	ss3834865301	Apr 27, 2020 (154)
30	SGDP_PRJ	ss3885739383	Apr 27, 2020 (154)
31	EVA	ss3986726901	Apr 26, 2021 (155)
32	TOPMED	ss5035785336	Apr 26, 2021 (155)
33	EVA	ss5237668983	Oct 16, 2022 (156)
34	1000G_HIGH_COVERAGE	ss5303113473	Oct 16, 2022 (156)
35	EVA	ss5427560132	Oct 16, 2022 (156)
36	1000G_HIGH_COVERAGE	ss5606824571	Oct 16, 2022 (156)
37	SANFORD_IMAGENETICS	ss5660093833	Oct 16, 2022 (156)
38	EVA	ss5833976470	Oct 16, 2022 (156)
39	EVA	ss5847797175	Oct 16, 2022 (156)
40	EVA	ss5848449282	Oct 16, 2022 (156)
41	EVA	ss5913937468	Oct 16, 2022 (156)
42	EVA	ss5951487659	Oct 16, 2022 (156)
43	EVA	ss5979506862	Oct 16, 2022 (156)
44	1000Genomes	NC_000017.10 - 39768820	Oct 12, 2018 (152)
45	1000Genomes_30x	NC_000017.11 - 41612568	Oct 16, 2022 (156)
46	The Avon Longitudinal Study of Parents and Children	NC_000017.10 - 39768820	Oct 12, 2018 (152)
47	ExAC	NC_000017.10 - 39768820	Oct 12, 2018 (152)
48	gnomAD - Genomes	NC_000017.11 - 41612568	Apr 26, 2021 (155)
49	gnomAD - Exomes Submission ignored due to conflicting rows: Row 12016419 (NC_000017.10:39768819:G:G 212947/216314, NC_000017.10:39768819:G:A 3367/216314) Row 12016420 (NC_000017.10:39768819:G:G 216313/216314, NC_000017.10:39768819:G:T 1/216314)	-	Jul 13, 2019 (153)
50	gnomAD - Exomes Submission ignored due to conflicting rows: Row 12016419 (NC_000017.10:39768819:G:G 212947/216314, NC_000017.10:39768819:G:A 3367/216314) Row 12016420 (NC_000017.10:39768819:G:G 216313/216314, NC_000017.10:39768819:G:T 1/216314)	-	Jul 13, 2019 (153)
51	GO Exome Sequencing Project	NC_000017.10 - 39768820	Oct 12, 2018 (152)
52	Genome of the Netherlands Release 5	NC_000017.10 - 39768820	Apr 27, 2020 (154)
53	Medical Genome Project healthy controls from Spanish population	NC_000017.10 - 39768820	Apr 27, 2020 (154)
54	Northern Sweden	NC_000017.10 - 39768820	Jul 13, 2019 (153)
55	SGDP_PRJ	NC_000017.10 - 39768820	Apr 27, 2020 (154)
56	Siberian	NC_000017.10 - 39768820	Apr 27, 2020 (154)
57	TopMed	NC_000017.11 - 41612568	Apr 26, 2021 (155)
58	UK 10K study - Twins	NC_000017.10 - 39768820	Oct 12, 2018 (152)
59	ALFA	NC_000017.11 - 41612568	Apr 26, 2021 (155)
60	ClinVar	RCV002132110.3	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).

Added to this RefSNP Cluster:

Submission IDs	Observation SPDI	Canonical SPDI	Source RSIDs
ss168146232, ss255635119, ss491736580, ss1697145741	NC_000017.9:37022345:G:A	NC_000017.11:41612567:G:A	(self)
71874638, 39837302, 3219280, 1570508, 17755897, 576468, 15307222, 37756363, 10044852, 39837302, ss339693262, ss491522429, ss536516043, ss713384085, ss993103370, ss1358633856, ss1635642899, ss1678636932, ss1692776069, ss1711460708, ss2029059417, ss2157528498, ss2742712175, ss2749773369, ss2949801718, ss2985095326, ss3015524816, ss3351744822, ss3627668343, ss3653867131, ss3742022357, ss3825113406, ss3834865301, ss3885739383, ss3986726901, ss5427560132, ss5660093833, ss5833976470, ss5847797175, ss5848449282, ss5951487659, ss5979506862	NC_000017.10:39768819:G:A	NC_000017.11:41612567:G:A	(self)
RCV002132110.3, 94350506, 507068669, 251330998, 13517917527, ss3700455167, ss3819931558, ss5035785336, ss5237668983, ss5303113473, ss5606824571, ss5913937468	NC_000017.11:41612567:G:A	NC_000017.11:41612567:G:A	(self)
ss2749773369, ss2949801718	NC_000017.10:39768819:G:C	NC_000017.11:41612567:G:C	(self)
ss2742712175	NC_000017.10:39768819:G:T	NC_000017.11:41612567:G: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 rs111383277

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

rs111383277