Name: rs74045023
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.

rs74045023

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr1:961570 (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>A / C>T
Variation Type: SNV Single Nucleotide Variation
Frequency: A=0.007258 (848/116834, ExAC)
A=0.00346 (111/32106, ALFA)
A=0.02177 (283/12998, GO-ESP) (+ 8 more)
A=0.0256 (164/6404, 1000G_30x)
A=0.0236 (118/5008, 1000G)
A=0.0002 (1/4480, Estonian)
A=0.0010 (4/3854, ALSPAC)
A=0.0013 (5/3708, TWINSUK)
A=0.019 (4/216, Qatari)
C=0.5 (4/8, SGDP_PRJ)
A=0.5 (4/8, SGDP_PRJ)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: KLHL17 : 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	32106	C=0.99654	A=0.00346, T=0.00000
European	Sub	24834	C=0.99903	A=0.00097, T=0.00000
African	Sub	3262	C=0.9776	A=0.0224, T=0.0000
African Others	Sub	116	C=0.966	A=0.034, T=0.000
African American	Sub	3146	C=0.9781	A=0.0219, T=0.0000
Asian	Sub	168	C=1.000	A=0.000, T=0.000
East Asian	Sub	112	C=1.000	A=0.000, T=0.000
Other Asian	Sub	56	C=1.00	A=0.00, T=0.00
Latin American 1	Sub	138	C=1.000	A=0.000, T=0.000
Latin American 2	Sub	604	C=1.000	A=0.000, T=0.000
South Asian	Sub	98	C=1.00	A=0.00, T=0.00
Other	Sub	3002	C=0.9953	A=0.0047, T=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
ExAC	Global	Study-wide	116834	C=0.992742	A=0.007258
ExAC	Europe	Sub	70076	C=0.99862	A=0.00138
ExAC	Asian	Sub	24910	C=0.99992	A=0.00008
ExAC	American	Sub	11396	C=0.99359	A=0.00641
ExAC	African	Sub	9598	C=0.9301	A=0.0699
ExAC	Other	Sub	854	C=0.994	A=0.006
Allele Frequency Aggregator	Total	Global	32106	C=0.99654	A=0.00346, T=0.00000
Allele Frequency Aggregator	European	Sub	24834	C=0.99903	A=0.00097, T=0.00000
Allele Frequency Aggregator	African	Sub	3262	C=0.9776	A=0.0224, T=0.0000
Allele Frequency Aggregator	Other	Sub	3002	C=0.9953	A=0.0047, T=0.0000
Allele Frequency Aggregator	Latin American 2	Sub	604	C=1.000	A=0.000, T=0.000
Allele Frequency Aggregator	Asian	Sub	168	C=1.000	A=0.000, T=0.000
Allele Frequency Aggregator	Latin American 1	Sub	138	C=1.000	A=0.000, T=0.000
Allele Frequency Aggregator	South Asian	Sub	98	C=1.00	A=0.00, T=0.00
GO Exome Sequencing Project	Global	Study-wide	12998	C=0.97823	A=0.02177
GO Exome Sequencing Project	European American	Sub	8592	C=0.9987	A=0.0013
GO Exome Sequencing Project	African American	Sub	4406	C=0.9383	A=0.0617
1000Genomes_30x	Global	Study-wide	6404	C=0.9744	A=0.0256
1000Genomes_30x	African	Sub	1786	C=0.9205	A=0.0795
1000Genomes_30x	Europe	Sub	1266	C=0.9945	A=0.0055
1000Genomes_30x	South Asian	Sub	1202	C=1.0000	A=0.0000
1000Genomes_30x	East Asian	Sub	1170	C=1.0000	A=0.0000
1000Genomes_30x	American	Sub	980	C=0.985	A=0.015
1000Genomes	Global	Study-wide	5008	C=0.9764	A=0.0236
1000Genomes	African	Sub	1322	C=0.9228	A=0.0772
1000Genomes	East Asian	Sub	1008	C=1.0000	A=0.0000
1000Genomes	Europe	Sub	1006	C=0.9950	A=0.0050
1000Genomes	South Asian	Sub	978	C=1.000	A=0.000
1000Genomes	American	Sub	694	C=0.984	A=0.016
Genetic variation in the Estonian population	Estonian	Study-wide	4480	C=0.9998	A=0.0002
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	C=0.9990	A=0.0010
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	C=0.9987	A=0.0013
Qatari	Global	Study-wide	216	C=0.981	A=0.019
SGDP_PRJ	Global	Study-wide	8	C=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 1	NC_000001.11:g.961570C>A
GRCh38.p14 chr 1	NC_000001.11:g.961570C>T
GRCh37.p13 chr 1	NC_000001.10:g.896950C>A
GRCh37.p13 chr 1	NC_000001.10:g.896950C>T
KLHL17 RefSeqGene	NG_027546.1:g.5984C>A
KLHL17 RefSeqGene	NG_027546.1:g.5984C>T

Gene: KLHL17, kelch like family member 17 (plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
KLHL17 transcript	NM_198317.3:c.367+18C>A	N/A	Intron Variant
KLHL17 transcript variant X3	XM_006710600.4:c.211+18C>A	N/A	Intron Variant
KLHL17 transcript variant X5	XM_006710601.4:c.211+18C>A	N/A	Intron Variant
KLHL17 transcript variant X1	XM_047419224.1:c.211+18C>A	N/A	Intron Variant
KLHL17 transcript variant X2	XM_047419225.1:c.211+18C>A	N/A	Intron Variant
KLHL17 transcript variant X4	XM_047419226.1:c.211+18C>A	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=	A	T
GRCh38.p14 chr 1	NC_000001.11:g.961570=	NC_000001.11:g.961570C>A	NC_000001.11:g.961570C>T
GRCh37.p13 chr 1	NC_000001.10:g.896950=	NC_000001.10:g.896950C>A	NC_000001.10:g.896950C>T
KLHL17 RefSeqGene	NG_027546.1:g.5984=	NG_027546.1:g.5984C>A	NG_027546.1:g.5984C>T
KLHL17 transcript	NM_198317.2:c.367+18=	NM_198317.2:c.367+18C>A	NM_198317.2:c.367+18C>T
KLHL17 transcript	NM_198317.3:c.367+18=	NM_198317.3:c.367+18C>A	NM_198317.3:c.367+18C>T
KLHL17 transcript variant X1	XM_005244744.1:c.211+18=	XM_005244744.1:c.211+18C>A	XM_005244744.1:c.211+18C>T
KLHL17 transcript variant X3	XM_006710600.4:c.211+18=	XM_006710600.4:c.211+18C>A	XM_006710600.4:c.211+18C>T
KLHL17 transcript variant X5	XM_006710601.4:c.211+18=	XM_006710601.4:c.211+18C>A	XM_006710601.4:c.211+18C>T
KLHL17 transcript variant X1	XM_047419224.1:c.211+18=	XM_047419224.1:c.211+18C>A	XM_047419224.1:c.211+18C>T
KLHL17 transcript variant X2	XM_047419225.1:c.211+18=	XM_047419225.1:c.211+18C>A	XM_047419225.1:c.211+18C>T
KLHL17 transcript variant X4	XM_047419226.1:c.211+18=	XM_047419226.1:c.211+18C>A	XM_047419226.1:c.211+18C>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#.

42 SubSNP, 16 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	ILLUMINA-UK	ss118439215	Feb 14, 2009 (130)
2	1000GENOMES	ss218191144	Jul 14, 2010 (132)
3	ILLUMINA	ss480826247	May 04, 2012 (137)
4	ILLUMINA	ss482426508	May 04, 2012 (137)
5	1000GENOMES	ss489714146	May 04, 2012 (137)
6	CLINSEQ_SNP	ss491581698	May 04, 2012 (137)
7	TISHKOFF	ss553711631	Apr 25, 2013 (138)
8	NHLBI-ESP	ss712260559	Apr 25, 2013 (138)
9	ILLUMINA	ss781327860	Sep 08, 2015 (146)
10	JMKIDD_LAB	ss974432447	Aug 21, 2014 (142)
11	EVA-GONL	ss974770544	Aug 21, 2014 (142)
12	1000GENOMES	ss1289344116	Aug 21, 2014 (142)
13	EVA_UK10K_ALSPAC	ss1599380006	Apr 01, 2015 (144)
14	EVA_UK10K_TWINSUK	ss1642374039	Apr 01, 2015 (144)
15	EVA_EXAC	ss1685219685	Apr 01, 2015 (144)
16	HAMMER_LAB	ss1793713250	Sep 08, 2015 (146)
17	WEILL_CORNELL_DGM	ss1917962041	Feb 12, 2016 (147)
18	HUMAN_LONGEVITY	ss2159373467	Dec 20, 2016 (150)
19	ILLUMINA	ss2632465573	Nov 08, 2017 (151)
20	GNOMAD	ss2730990249	Nov 08, 2017 (151)
21	GNOMAD	ss2746170622	Nov 08, 2017 (151)
22	GNOMAD	ss2750653756	Nov 08, 2017 (151)
23	ILLUMINA	ss3641566231	Oct 11, 2018 (152)
24	EGCUT_WGS	ss3654262910	Jul 12, 2019 (153)
25	EVA_DECODE	ss3685994439	Jul 12, 2019 (153)
26	KHV_HUMAN_GENOMES	ss3798745079	Jul 12, 2019 (153)
27	EVA	ss3823541776	Apr 25, 2020 (154)
28	EVA	ss3825548929	Apr 25, 2020 (154)
29	EVA	ss3825981945	Apr 25, 2020 (154)
30	SGDP_PRJ	ss3847999199	Apr 25, 2020 (154)
31	FSA-LAB	ss3983910333	Apr 25, 2021 (155)
32	EVA	ss3986090708	Apr 25, 2021 (155)
33	TOPMED	ss4436471269	Apr 25, 2021 (155)
34	TOPMED	ss4436471270	Apr 25, 2021 (155)
35	1000G_HIGH_COVERAGE	ss5240867911	Oct 12, 2022 (156)
36	EVA	ss5316190893	Oct 12, 2022 (156)
37	HUGCELL_USP	ss5442115549	Oct 12, 2022 (156)
38	1000G_HIGH_COVERAGE	ss5512494354	Oct 12, 2022 (156)
39	SANFORD_IMAGENETICS	ss5624752181	Oct 12, 2022 (156)
40	EVA	ss5831420340	Oct 12, 2022 (156)
41	EVA	ss5906708909	Oct 12, 2022 (156)
42	EVA	ss5936584778	Oct 12, 2022 (156)
43	1000Genomes	NC_000001.10 - 896950	Oct 11, 2018 (152)
44	1000Genomes_30x	NC_000001.11 - 961570	Oct 12, 2022 (156)
45	The Avon Longitudinal Study of Parents and Children	NC_000001.10 - 896950	Oct 11, 2018 (152)
46	Genetic variation in the Estonian population	NC_000001.10 - 896950	Oct 11, 2018 (152)
47	ExAC	NC_000001.10 - 896950	Oct 11, 2018 (152)
48	gnomAD - Genomes Submission ignored due to conflicting rows: Row 98066 (NC_000001.11:961569:C:A 3155/140300) Row 98067 (NC_000001.11:961569:C:T 1/140308)	-	Apr 25, 2021 (155)
49	gnomAD - Genomes Submission ignored due to conflicting rows: Row 98066 (NC_000001.11:961569:C:A 3155/140300) Row 98067 (NC_000001.11:961569:C:T 1/140308)	-	Apr 25, 2021 (155)
50	gnomAD - Exomes Submission ignored due to conflicting rows: Row 4852 (NC_000001.10:896949:C:C 242613/244160, NC_000001.10:896949:C:A 1547/244160) Row 4853 (NC_000001.10:896949:C:C 244157/244160, NC_000001.10:896949:C:T 3/244160)	-	Jul 12, 2019 (153)
51	gnomAD - Exomes Submission ignored due to conflicting rows: Row 4852 (NC_000001.10:896949:C:C 242613/244160, NC_000001.10:896949:C:A 1547/244160) Row 4853 (NC_000001.10:896949:C:C 244157/244160, NC_000001.10:896949:C:T 3/244160)	-	Jul 12, 2019 (153)
52	GO Exome Sequencing Project	NC_000001.10 - 896950	Oct 11, 2018 (152)
53	Qatari	NC_000001.10 - 896950	Apr 25, 2020 (154)
54	SGDP_PRJ	NC_000001.10 - 896950	Apr 25, 2020 (154)
55	TopMed Submission ignored due to conflicting rows: Row 77604 (NC_000001.11:961569:C:A 6386/264690) Row 77605 (NC_000001.11:961569:C:T 4/264690)	-	Apr 25, 2021 (155)
56	TopMed Submission ignored due to conflicting rows: Row 77604 (NC_000001.11:961569:C:A 6386/264690) Row 77605 (NC_000001.11:961569:C:T 4/264690)	-	Apr 25, 2021 (155)
57	UK 10K study - Twins	NC_000001.10 - 896950	Oct 11, 2018 (152)
58	ALFA	NC_000001.11 - 961570	Apr 25, 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
ss118439215, ss482426508, ss491581698	NC_000001.9:886812:C:A	NC_000001.11:961569:C:A	(self)
9041, 2148, 1158, 4392969, 513, 3971, 16179, 2148, ss218191144, ss480826247, ss489714146, ss553711631, ss712260559, ss781327860, ss974432447, ss974770544, ss1289344116, ss1599380006, ss1642374039, ss1685219685, ss1793713250, ss1917962041, ss2632465573, ss2730990249, ss2746170622, ss2750653756, ss3641566231, ss3654262910, ss3823541776, ss3825548929, ss3825981945, ss3847999199, ss3983910333, ss3986090708, ss5316190893, ss5624752181, ss5831420340, ss5936584778	NC_000001.10:896949:C:A	NC_000001.11:961569:C:A	(self)
20289, 4259201382, ss2159373467, ss3685994439, ss3798745079, ss4436471269, ss5240867911, ss5442115549, ss5512494354, ss5906708909	NC_000001.11:961569:C:A	NC_000001.11:961569:C:A	(self)
ss2730990249, ss2746170622, ss2750653756	NC_000001.10:896949:C:T	NC_000001.11:961569:C:T	(self)
4259201382, ss4436471270	NC_000001.11:961569:C:T	NC_000001.11:961569: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 rs74045023

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

rs74045023