Name: rs75928378
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.

rs75928378

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr1:66820539 (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: T>A / T>C
Variation Type: SNV Single Nucleotide Variation
Frequency: C=0.061298 (16225/264690, TOPMED)
C=0.059493 (8326/139950, GnomAD)
C=0.00042 (12/28258, 14KJPN) (+ 16 more)
C=0.06419 (1205/18772, ALFA)
C=0.00018 (3/16760, 8.3KJPN)
C=0.0401 (257/6404, 1000G_30x)
C=0.0379 (190/5008, 1000G)
C=0.0592 (265/4480, Estonian)
C=0.0976 (376/3854, ALSPAC)
C=0.0863 (320/3708, TWINSUK)
C=0.0014 (4/2922, KOREAN)
C=0.0022 (4/1832, Korea1K)
C=0.100 (100/998, GoNL)
C=0.067 (40/600, NorthernSweden)
C=0.120 (26/216, Qatari)
T=0.45 (28/62, SGDP_PRJ)
C=0.12 (5/40, GENOME_DK)
T=0.5 (3/6, Siberian)
C=0.5 (3/6, Siberian)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: DNAI4 : 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: 20231103111315

Population	Group	Sample Size	Ref Allele	Alt Allele	Ref HMOZ	Alt HMOZ	HTRZ	HWEP
Total	Global	18772	T=0.93581	A=0.00000, C=0.06419	0.876412	0.004794	0.118794	1
European	Sub	14190	T=0.92382	A=0.00000, C=0.07618	0.853559	0.00592	0.140521	0
African	Sub	2924	T=0.9880	A=0.0000, C=0.0120	0.97606	0.0	0.02394	0
African Others	Sub	114	T=1.000	A=0.000, C=0.000	1.0	0.0	0.0	N/A
African American	Sub	2810	T=0.9875	A=0.0000, C=0.0125	0.975089	0.0	0.024911	0
Asian	Sub	112	T=0.991	A=0.000, C=0.009	0.982143	0.0	0.017857	0
East Asian	Sub	86	T=0.99	A=0.00, C=0.01	0.976744	0.0	0.023256	0
Other Asian	Sub	26	T=1.00	A=0.00, C=0.00	1.0	0.0	0.0	N/A
Latin American 1	Sub	146	T=0.938	A=0.000, C=0.062	0.90411	0.027397	0.068493	7
Latin American 2	Sub	610	T=0.948	A=0.000, C=0.052	0.895082	0.0	0.104918	1
South Asian	Sub	98	T=0.91	A=0.00, C=0.09	0.816327	0.0	0.183673	0
Other	Sub	692	T=0.945	A=0.000, C=0.055	0.893064	0.00289	0.104046	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	T=0.938702	C=0.061298
gnomAD - Genomes	Global	Study-wide	139950	T=0.940507	C=0.059493
gnomAD - Genomes	European	Sub	75722	T=0.91755	C=0.08245
gnomAD - Genomes	African	Sub	41990	T=0.98014	C=0.01986
gnomAD - Genomes	American	Sub	13634	T=0.93641	C=0.06359
gnomAD - Genomes	Ashkenazi Jewish	Sub	3322	T=0.9259	C=0.0741
gnomAD - Genomes	East Asian	Sub	3132	T=0.9968	C=0.0032
gnomAD - Genomes	Other	Sub	2150	T=0.9414	C=0.0586
14KJPN	JAPANESE	Study-wide	28258	T=0.99958	C=0.00042
Allele Frequency Aggregator	Total	Global	18772	T=0.93581	A=0.00000, C=0.06419
Allele Frequency Aggregator	European	Sub	14190	T=0.92382	A=0.00000, C=0.07618
Allele Frequency Aggregator	African	Sub	2924	T=0.9880	A=0.0000, C=0.0120
Allele Frequency Aggregator	Other	Sub	692	T=0.945	A=0.000, C=0.055
Allele Frequency Aggregator	Latin American 2	Sub	610	T=0.948	A=0.000, C=0.052
Allele Frequency Aggregator	Latin American 1	Sub	146	T=0.938	A=0.000, C=0.062
Allele Frequency Aggregator	Asian	Sub	112	T=0.991	A=0.000, C=0.009
Allele Frequency Aggregator	South Asian	Sub	98	T=0.91	A=0.00, C=0.09
8.3KJPN	JAPANESE	Study-wide	16760	T=0.99982	C=0.00018
1000Genomes_30x	Global	Study-wide	6404	T=0.9599	C=0.0401
1000Genomes_30x	African	Sub	1786	T=0.9905	C=0.0095
1000Genomes_30x	Europe	Sub	1266	T=0.9297	C=0.0703
1000Genomes_30x	South Asian	Sub	1202	T=0.9201	C=0.0799
1000Genomes_30x	East Asian	Sub	1170	T=0.9932	C=0.0068
1000Genomes_30x	American	Sub	980	T=0.952	C=0.048
1000Genomes	Global	Study-wide	5008	T=0.9621	C=0.0379
1000Genomes	African	Sub	1322	T=0.9917	C=0.0083
1000Genomes	East Asian	Sub	1008	T=0.9950	C=0.0050
1000Genomes	Europe	Sub	1006	T=0.9215	C=0.0785
1000Genomes	South Asian	Sub	978	T=0.933	C=0.067
1000Genomes	American	Sub	694	T=0.958	C=0.042
Genetic variation in the Estonian population	Estonian	Study-wide	4480	T=0.9408	C=0.0592
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	T=0.9024	C=0.0976
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	T=0.9137	C=0.0863
KOREAN population from KRGDB	KOREAN	Study-wide	2922	T=0.9986	C=0.0014
Korean Genome Project	KOREAN	Study-wide	1832	T=0.9978	C=0.0022
Genome of the Netherlands Release 5	Genome of the Netherlands	Study-wide	998	T=0.900	C=0.100
Northern Sweden	ACPOP	Study-wide	600	T=0.933	C=0.067
Qatari	Global	Study-wide	216	T=0.880	C=0.120
SGDP_PRJ	Global	Study-wide	62	T=0.45	C=0.55
The Danish reference pan genome	Danish	Study-wide	40	T=0.88	C=0.12
Siberian	Global	Study-wide	6	T=0.5	C=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.66820539T>A
GRCh38.p14 chr 1	NC_000001.11:g.66820539T>C
GRCh37.p13 chr 1	NC_000001.10:g.67286222T>A
GRCh37.p13 chr 1	NC_000001.10:g.67286222T>C

Gene: DNAI4, dynein axonemal intermediate chain 4 (minus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
DNAI4 transcript variant 1	NM_024763.5:c.2496+1822A>T	N/A	Intron Variant
DNAI4 transcript variant 2	NM_207014.3:c.	N/A	Genic Downstream Transcript Variant
DNAI4 transcript variant X4	XM_005271212.4:c.2301+182… XM_005271212.4:c.2301+1822A>T	N/A	Intron Variant
DNAI4 transcript variant X1	XM_011542161.3:c.2409+182… XM_011542161.3:c.2409+1822A>T	N/A	Intron Variant
DNAI4 transcript variant X2	XM_011542162.3:c.2397+182… XM_011542162.3:c.2397+1822A>T	N/A	Intron Variant
DNAI4 transcript variant X7	XM_017002353.2:c.2202+182… XM_017002353.2:c.2202+1822A>T	N/A	Intron Variant
DNAI4 transcript variant X8	XM_017002354.2:c.2115+182… XM_017002354.2:c.2115+1822A>T	N/A	Intron Variant
DNAI4 transcript variant X9	XM_017002355.1:c.1734+182… XM_017002355.1:c.1734+1822A>T	N/A	Intron Variant
DNAI4 transcript variant X10	XM_024449821.2:c.1629+182… XM_024449821.2:c.1629+1822A>T	N/A	Intron Variant
DNAI4 transcript variant X3	XM_047430731.1:c.2310+182… XM_047430731.1:c.2310+1822A>T	N/A	Intron Variant
DNAI4 transcript variant X5	XM_047430749.1:c.2280+182… XM_047430749.1:c.2280+1822A>T	N/A	Intron Variant
DNAI4 transcript variant X6	XM_047430752.1:c.2214+182… XM_047430752.1:c.2214+1822A>T	N/A	Intron Variant
DNAI4 transcript variant X11	XM_017002357.2:c.	N/A	Genic Downstream Transcript 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	T=	A	C
GRCh38.p14 chr 1	NC_000001.11:g.66820539=	NC_000001.11:g.66820539T>A	NC_000001.11:g.66820539T>C
GRCh37.p13 chr 1	NC_000001.10:g.67286222=	NC_000001.10:g.67286222T>A	NC_000001.10:g.67286222T>C
WDR78 transcript variant 1	NM_024763.4:c.2496+1822=	NM_024763.4:c.2496+1822A>T	NM_024763.4:c.2496+1822A>G
DNAI4 transcript variant 1	NM_024763.5:c.2496+1822=	NM_024763.5:c.2496+1822A>T	NM_024763.5:c.2496+1822A>G
WDR78 transcript variant X1	XM_005271212.1:c.2301+1822=	XM_005271212.1:c.2301+1822A>T	XM_005271212.1:c.2301+1822A>G
DNAI4 transcript variant X4	XM_005271212.4:c.2301+1822=	XM_005271212.4:c.2301+1822A>T	XM_005271212.4:c.2301+1822A>G
WDR78 transcript variant X4	XM_005271213.1:c.1629+1822=	XM_005271213.1:c.1629+1822A>T	XM_005271213.1:c.1629+1822A>G
DNAI4 transcript variant X1	XM_011542161.3:c.2409+1822=	XM_011542161.3:c.2409+1822A>T	XM_011542161.3:c.2409+1822A>G
DNAI4 transcript variant X2	XM_011542162.3:c.2397+1822=	XM_011542162.3:c.2397+1822A>T	XM_011542162.3:c.2397+1822A>G
DNAI4 transcript variant X7	XM_017002353.2:c.2202+1822=	XM_017002353.2:c.2202+1822A>T	XM_017002353.2:c.2202+1822A>G
DNAI4 transcript variant X8	XM_017002354.2:c.2115+1822=	XM_017002354.2:c.2115+1822A>T	XM_017002354.2:c.2115+1822A>G
DNAI4 transcript variant X9	XM_017002355.1:c.1734+1822=	XM_017002355.1:c.1734+1822A>T	XM_017002355.1:c.1734+1822A>G
DNAI4 transcript variant X10	XM_024449821.2:c.1629+1822=	XM_024449821.2:c.1629+1822A>T	XM_024449821.2:c.1629+1822A>G
DNAI4 transcript variant X3	XM_047430731.1:c.2310+1822=	XM_047430731.1:c.2310+1822A>T	XM_047430731.1:c.2310+1822A>G
DNAI4 transcript variant X5	XM_047430749.1:c.2280+1822=	XM_047430749.1:c.2280+1822A>T	XM_047430749.1:c.2280+1822A>G
DNAI4 transcript variant X6	XM_047430752.1:c.2214+1822=	XM_047430752.1:c.2214+1822A>T	XM_047430752.1:c.2214+1822A>G

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#.

38 SubSNP, 18 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	1000GENOMES	ss230568198	Jul 14, 2010 (132)
2	SSMP	ss648079744	Apr 25, 2013 (138)
3	EVA-GONL	ss975246686	Aug 21, 2014 (142)
4	JMKIDD_LAB	ss1067953618	Aug 21, 2014 (142)
5	1000GENOMES	ss1291220648	Aug 21, 2014 (142)
6	DDI	ss1425837346	Apr 01, 2015 (144)
7	EVA_GENOME_DK	ss1574120535	Apr 01, 2015 (144)
8	EVA_DECODE	ss1584616108	Apr 01, 2015 (144)
9	EVA_UK10K_ALSPAC	ss1600348998	Apr 01, 2015 (144)
10	EVA_UK10K_TWINSUK	ss1643343031	Apr 01, 2015 (144)
11	WEILL_CORNELL_DGM	ss1918454698	Feb 12, 2016 (147)
12	JJLAB	ss2019744694	Sep 14, 2016 (149)
13	USC_VALOUEV	ss2147760454	Dec 20, 2016 (150)
14	HUMAN_LONGEVITY	ss2163188142	Dec 20, 2016 (150)
15	GRF	ss2697678090	Nov 08, 2017 (151)
16	GNOMAD	ss2756073106	Nov 08, 2017 (151)
17	AFFY	ss2985515303	Nov 08, 2017 (151)
18	SWEGEN	ss2986948359	Nov 08, 2017 (151)
19	BIOINF_KMB_FNS_UNIBA	ss3023634129	Nov 08, 2017 (151)
20	CSHL	ss3343492804	Nov 08, 2017 (151)
21	EGCUT_WGS	ss3655018336	Jul 12, 2019 (153)
22	EVA_DECODE	ss3686933363	Jul 12, 2019 (153)
23	ACPOP	ss3727119261	Jul 12, 2019 (153)
24	EVA	ss3746306322	Jul 12, 2019 (153)
25	SGDP_PRJ	ss3849019081	Apr 25, 2020 (154)
26	KRGDB	ss3894046537	Apr 25, 2020 (154)
27	KOGIC	ss3944672918	Apr 25, 2020 (154)
28	TOPMED	ss4452628708	Apr 25, 2021 (155)
29	TOMMO_GENOMICS	ss5144317525	Apr 25, 2021 (155)
30	1000G_HIGH_COVERAGE	ss5242553830	Oct 12, 2022 (156)
31	HUGCELL_USP	ss5443588480	Oct 12, 2022 (156)
32	1000G_HIGH_COVERAGE	ss5514973688	Oct 12, 2022 (156)
33	SANFORD_IMAGENETICS	ss5625692410	Oct 12, 2022 (156)
34	TOMMO_GENOMICS	ss5669194673	Oct 12, 2022 (156)
35	YY_MCH	ss5800668162	Oct 12, 2022 (156)
36	EVA	ss5832070288	Oct 12, 2022 (156)
37	EVA	ss5908589591	Oct 12, 2022 (156)
38	EVA	ss5937531050	Oct 12, 2022 (156)
39	1000Genomes	NC_000001.10 - 67286222	Oct 11, 2018 (152)
40	1000Genomes_30x	NC_000001.11 - 66820539	Oct 12, 2022 (156)
41	The Avon Longitudinal Study of Parents and Children	NC_000001.10 - 67286222	Oct 11, 2018 (152)
42	Genetic variation in the Estonian population	NC_000001.10 - 67286222	Oct 11, 2018 (152)
43	The Danish reference pan genome	NC_000001.10 - 67286222	Apr 25, 2020 (154)
44	gnomAD - Genomes	NC_000001.11 - 66820539	Apr 25, 2021 (155)
45	Genome of the Netherlands Release 5	NC_000001.10 - 67286222	Apr 25, 2020 (154)
46	KOREAN population from KRGDB	NC_000001.10 - 67286222	Apr 25, 2020 (154)
47	Korean Genome Project	NC_000001.11 - 66820539	Apr 25, 2020 (154)
48	Northern Sweden	NC_000001.10 - 67286222	Jul 12, 2019 (153)
49	Qatari	NC_000001.10 - 67286222	Apr 25, 2020 (154)
50	SGDP_PRJ	NC_000001.10 - 67286222	Apr 25, 2020 (154)
51	Siberian	NC_000001.10 - 67286222	Apr 25, 2020 (154)
52	8.3KJPN	NC_000001.10 - 67286222	Apr 25, 2021 (155)
53	14KJPN	NC_000001.11 - 66820539	Oct 12, 2022 (156)
54	TopMed	NC_000001.11 - 66820539	Apr 25, 2021 (155)
55	UK 10K study - Twins	NC_000001.10 - 67286222	Oct 11, 2018 (152)
56	ALFA	NC_000001.11 - 66820539	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
11190800331	NC_000001.11:66820538:T:A	NC_000001.11:66820538:T:A	(self)
ss1584616108	NC_000001.9:67058809:T:C	NC_000001.11:66820538:T:C	(self)
1950690, 1068706, 756584, 1536116, 456192, 1223931, 404126, 496628, 1036061, 276808, 2286832, 1068706, ss230568198, ss648079744, ss975246686, ss1067953618, ss1291220648, ss1425837346, ss1574120535, ss1600348998, ss1643343031, ss1918454698, ss2019744694, ss2147760454, ss2697678090, ss2756073106, ss2985515303, ss2986948359, ss3343492804, ss3655018336, ss3727119261, ss3746306322, ss3849019081, ss3894046537, ss5144317525, ss5625692410, ss5832070288, ss5937531050	NC_000001.10:67286221:T:C	NC_000001.11:66820538:T:C	(self)
2499623, 13755092, 1050919, 3031777, 16235043, 11190800331, ss2163188142, ss3023634129, ss3686933363, ss3944672918, ss4452628708, ss5242553830, ss5443588480, ss5514973688, ss5669194673, ss5800668162, ss5908589591	NC_000001.11:66820538:T:C	NC_000001.11:66820538:T: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 rs75928378

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

rs75928378