Name: rs74353715
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.

rs74353715

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr4:163113608-163113612 (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: delGT / dupGT
Variation Type: Indel Insertion and Deletion
Frequency: TGTGT=0.15450 (4366/28258, 14KJPN)
TGTGT=0.15203 (2548/16760, 8.3KJPN)
TGTGT=0.2071 (1326/6404, 1000G_30x) (+ 9 more)
TGTGT=0.3243 (1654/5100, ALFA)
TGTGT=0.2107 (1055/5008, 1000G)
TGTGT=0.2308 (1034/4480, Estonian)
TGTGT=0.2338 (901/3854, ALSPAC)
TGTGT=0.2241 (831/3708, TWINSUK)
TGTGT=0.1943 (356/1832, Korea1K)
TGTGT=0.213 (213/998, GoNL)
TGTGT=0.245 (147/600, NorthernSweden)
TGTGT=0.20 (8/40, GENOME_DK)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: NAF1 : Intron Variant
LOC101928081 : 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	5100	TGTGT=0.3243	TGT=0.0000, TGTGTGT=0.6757	0.163922	0.515294	0.320784	32
European	Sub	4834	TGTGT=0.2886	TGT=0.0000, TGTGTGT=0.7114	0.11957	0.542408	0.338022	32
African	Sub	184	TGTGT=1.000	TGT=0.000, TGTGTGT=0.000	1.0	0.0	0.0	N/A
African Others	Sub	0	TGTGT=0	TGT=0, TGTGTGT=0	0	0	0	N/A
African American	Sub	184	TGTGT=1.000	TGT=0.000, TGTGTGT=0.000	1.0	0.0	0.0	N/A
Asian	Sub	2	TGTGT=1.0	TGT=0.0, TGTGTGT=0.0	1.0	0.0	0.0	N/A
East Asian	Sub	0	TGTGT=0	TGT=0, TGTGTGT=0	0	0	0	N/A
Other Asian	Sub	2	TGTGT=1.0	TGT=0.0, TGTGTGT=0.0	1.0	0.0	0.0	N/A
Latin American 1	Sub	12	TGTGT=1.00	TGT=0.00, TGTGTGT=0.00	1.0	0.0	0.0	N/A
Latin American 2	Sub	36	TGTGT=1.00	TGT=0.00, TGTGTGT=0.00	1.0	0.0	0.0	N/A
South Asian	Sub	4	TGTGT=1.0	TGT=0.0, TGTGTGT=0.0	1.0	0.0	0.0	N/A
Other	Sub	28	TGTGT=0.75	TGT=0.00, TGTGTGT=0.25	0.714286	0.214286	0.071429	6

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
14KJPN	JAPANESE	Study-wide	28258	- No frequency provided	dupGT=0.84550
8.3KJPN	JAPANESE	Study-wide	16760	- No frequency provided	dupGT=0.84797
1000Genomes_30x	Global	Study-wide	6404	- No frequency provided	dupGT=0.7929
1000Genomes_30x	African	Sub	1786	- No frequency provided	dupGT=0.7895
1000Genomes_30x	Europe	Sub	1266	- No frequency provided	dupGT=0.7662
1000Genomes_30x	South Asian	Sub	1202	- No frequency provided	dupGT=0.8478
1000Genomes_30x	East Asian	Sub	1170	- No frequency provided	dupGT=0.7786
1000Genomes_30x	American	Sub	980	- No frequency provided	dupGT=0.784
Allele Frequency Aggregator	Total	Global	5100	TGTGT=0.3243	delGT=0.0000, dupGT=0.6757
Allele Frequency Aggregator	European	Sub	4834	TGTGT=0.2886	delGT=0.0000, dupGT=0.7114
Allele Frequency Aggregator	African	Sub	184	TGTGT=1.000	delGT=0.000, dupGT=0.000
Allele Frequency Aggregator	Latin American 2	Sub	36	TGTGT=1.00	delGT=0.00, dupGT=0.00
Allele Frequency Aggregator	Other	Sub	28	TGTGT=0.75	delGT=0.00, dupGT=0.25
Allele Frequency Aggregator	Latin American 1	Sub	12	TGTGT=1.00	delGT=0.00, dupGT=0.00
Allele Frequency Aggregator	South Asian	Sub	4	TGTGT=1.0	delGT=0.0, dupGT=0.0
Allele Frequency Aggregator	Asian	Sub	2	TGTGT=1.0	delGT=0.0, dupGT=0.0
1000Genomes	Global	Study-wide	5008	- No frequency provided	dupGT=0.7893
1000Genomes	African	Sub	1322	- No frequency provided	dupGT=0.7882
1000Genomes	East Asian	Sub	1008	- No frequency provided	dupGT=0.7847
1000Genomes	Europe	Sub	1006	- No frequency provided	dupGT=0.7604
1000Genomes	South Asian	Sub	978	- No frequency provided	dupGT=0.834
1000Genomes	American	Sub	694	- No frequency provided	dupGT=0.777
Genetic variation in the Estonian population	Estonian	Study-wide	4480	- No frequency provided	dupGT=0.7692
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	- No frequency provided	dupGT=0.7662
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	- No frequency provided	dupGT=0.7759
Korean Genome Project	KOREAN	Study-wide	1832	- No frequency provided	dupGT=0.8057
Genome of the Netherlands Release 5	Genome of the Netherlands	Study-wide	998	- No frequency provided	dupGT=0.787
Northern Sweden	ACPOP	Study-wide	600	- No frequency provided	dupGT=0.755
The Danish reference pan genome	Danish	Study-wide	40	- No frequency provided	dupGT=0.80

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 4	NC_000004.12:g.163113609GT[1]
GRCh38.p14 chr 4	NC_000004.12:g.163113609GT[3]
GRCh37.p13 chr 4	NC_000004.11:g.164034761GT[1]
GRCh37.p13 chr 4	NC_000004.11:g.164034761GT[3]

Gene: NAF1, nuclear assembly factor 1 ribonucleoprotein (minus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
NAF1 transcript variant 2	NM_001128931.2:c.	N/A	Genic Downstream Transcript Variant
NAF1 transcript variant 1	NM_138386.3:c.	N/A	Genic Downstream Transcript Variant
NAF1 transcript variant X1	XM_011532410.4:c.	N/A	Genic Downstream Transcript Variant
NAF1 transcript variant X6	XM_047416407.1:c.	N/A	Genic Downstream Transcript Variant
NAF1 transcript variant X7	XM_047416408.1:c.	N/A	Genic Downstream Transcript Variant
NAF1 transcript variant X3	XR_001741349.3:n.	N/A	Intron Variant
NAF1 transcript variant X2	XR_001741350.3:n.	N/A	Intron Variant
NAF1 transcript variant X4	XR_938798.4:n.	N/A	Intron Variant
NAF1 transcript variant X5	XR_938799.4:n.	N/A	Intron Variant

Gene: LOC101928081, uncharacterized LOC101928081 (plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
LOC101928081 transcript	XR_244745.4:n.	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	TGTGT=	delGT	dupGT
GRCh38.p14 chr 4	NC_000004.12:g.163113608_163113612=	NC_000004.12:g.163113609GT[1]	NC_000004.12:g.163113609GT[3]
GRCh37.p13 chr 4	NC_000004.11:g.164034760_164034764=	NC_000004.11:g.164034761GT[1]	NC_000004.11:g.164034761GT[3]

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#.

59 SubSNP, 14 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	HGSV	ss81702582	Dec 03, 2013 (138)
2	HGSV	ss81849911	Dec 04, 2013 (138)
3	BCMHGSC_JDW	ss103883656	Dec 06, 2013 (138)
4	GMI	ss154921674	Dec 01, 2009 (131)
5	GMI	ss154921682	Dec 06, 2013 (138)
6	BL	ss256038855	May 09, 2011 (135)
7	GMI	ss287761430	Dec 06, 2013 (138)
8	GMI	ss288593317	May 04, 2012 (137)
9	GMI	ss288593318	Oct 12, 2018 (152)
10	1000GENOMES	ss326601006	May 09, 2011 (135)
11	1000GENOMES	ss326637571	May 09, 2011 (135)
12	1000GENOMES	ss326827777	May 09, 2011 (135)
13	1000GENOMES	ss498934899	May 04, 2012 (137)
14	LUNTER	ss551439374	Apr 25, 2013 (138)
15	LUNTER	ss551578180	Apr 25, 2013 (138)
16	LUNTER	ss553173226	Apr 25, 2013 (138)
17	TISHKOFF	ss557572718	Oct 12, 2018 (152)
18	SSMP	ss663476333	Apr 01, 2015 (144)
19	BILGI_BIOE	ss666286834	Apr 25, 2013 (138)
20	EVA-GONL	ss980926269	Aug 21, 2014 (142)
21	1000GENOMES	ss1373063828	Aug 21, 2014 (142)
22	DDI	ss1536438373	Apr 01, 2015 (144)
23	EVA_GENOME_DK	ss1576388397	Apr 01, 2015 (144)
24	EVA_DECODE	ss1590442917	Apr 01, 2015 (144)
25	EVA_UK10K_ALSPAC	ss1704447385	Apr 01, 2015 (144)
26	EVA_UK10K_TWINSUK	ss1704448212	Apr 01, 2015 (144)
27	HAMMER_LAB	ss1802518341	Sep 08, 2015 (146)
28	GENOMED	ss1969929639	Jul 19, 2016 (147)
29	JJLAB	ss2030645480	Sep 14, 2016 (149)
30	SYSTEMSBIOZJU	ss2625830849	Nov 08, 2017 (151)
31	GNOMAD	ss2817929980	Nov 08, 2017 (151)
32	SWEGEN	ss2995932289	Nov 08, 2017 (151)
33	MCHAISSO	ss3065001116	Nov 08, 2017 (151)
34	BEROUKHIMLAB	ss3644170593	Oct 12, 2018 (152)
35	BIOINF_KMB_FNS_UNIBA	ss3645840383	Oct 12, 2018 (152)
36	EGCUT_WGS	ss3663846862	Jul 13, 2019 (153)
37	EVA_DECODE	ss3713516130	Jul 13, 2019 (153)
38	ACPOP	ss3731812195	Jul 13, 2019 (153)
39	PACBIO	ss3784928690	Jul 13, 2019 (153)
40	PACBIO	ss3790355327	Jul 13, 2019 (153)
41	PACBIO	ss3795230955	Jul 13, 2019 (153)
42	KHV_HUMAN_GENOMES	ss3805855686	Jul 13, 2019 (153)
43	EVA	ss3828928599	Apr 26, 2020 (154)
44	EVA	ss3837915960	Apr 26, 2020 (154)
45	EVA	ss3843356936	Apr 26, 2020 (154)
46	KOGIC	ss3955556629	Apr 26, 2020 (154)
47	GNOMAD	ss4124495701	Apr 26, 2021 (155)
48	TOMMO_GENOMICS	ss5169058341	Apr 26, 2021 (155)
49	1000G_HIGH_COVERAGE	ss5261838700	Oct 13, 2022 (156)
50	HUGCELL_USP	ss5460307964	Oct 13, 2022 (156)
51	EVA	ss5507819085	Oct 13, 2022 (156)
52	1000G_HIGH_COVERAGE	ss5544376105	Oct 13, 2022 (156)
53	SANFORD_IMAGENETICS	ss5636570821	Oct 13, 2022 (156)
54	TOMMO_GENOMICS	ss5704340644	Oct 13, 2022 (156)
55	YY_MCH	ss5805741489	Oct 13, 2022 (156)
56	EVA	ss5845036239	Oct 13, 2022 (156)
57	EVA	ss5854543968	Oct 13, 2022 (156)
58	EVA	ss5866436433	Oct 13, 2022 (156)
59	EVA	ss5964980492	Oct 13, 2022 (156)
60	1000Genomes	NC_000004.11 - 164034760	Oct 12, 2018 (152)
61	1000Genomes_30x	NC_000004.12 - 163113608	Oct 13, 2022 (156)
62	The Avon Longitudinal Study of Parents and Children	NC_000004.11 - 164034760	Oct 12, 2018 (152)
63	Genetic variation in the Estonian population	NC_000004.11 - 164034760	Oct 12, 2018 (152)
64	The Danish reference pan genome	NC_000004.11 - 164034760	Apr 26, 2020 (154)
65	gnomAD - Genomes Submission ignored due to conflicting rows: Row 171800682 (NC_000004.12:163113607::TG 108495/139786) Row 171800684 (NC_000004.12:163113607:TG: 1/139842)	-	Apr 26, 2021 (155)
66	gnomAD - Genomes Submission ignored due to conflicting rows: Row 171800682 (NC_000004.12:163113607::TG 108495/139786) Row 171800684 (NC_000004.12:163113607:TG: 1/139842)	-	Apr 26, 2021 (155)
67	Genome of the Netherlands Release 5	NC_000004.11 - 164034760	Apr 26, 2020 (154)
68	Korean Genome Project	NC_000004.12 - 163113608	Apr 26, 2020 (154)
69	Northern Sweden	NC_000004.11 - 164034760	Jul 13, 2019 (153)
70	8.3KJPN	NC_000004.11 - 164034760	Apr 26, 2021 (155)
71	14KJPN	NC_000004.12 - 163113608	Oct 13, 2022 (156)
72	UK 10K study - Twins	NC_000004.11 - 164034760	Oct 12, 2018 (152)
73	ALFA	NC_000004.12 - 163113608	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).

Associated ID	History Updated (Build)
rs141512732	Sep 17, 2011 (135)

Added to this RefSNP Cluster:

Submission IDs	Observation SPDI	Canonical SPDI	Source RSIDs
ss4124495701	NC_000004.12:163113607:TG:	NC_000004.12:163113607:TGTGT:TGT	(self)
935462061	NC_000004.12:163113607:TGTGT:TGT	NC_000004.12:163113607:TGTGT:TGT	(self)
ss256038855, ss288593317, ss326601006, ss326637571, ss326827777, ss551439374, ss551578180, ss553173226, ss1590442917	NC_000004.10:164254209::TG	NC_000004.12:163113607:TGTGT:TGTGT… NC_000004.12:163113607:TGTGT:TGTGTGT	(self)
ss288593318	NC_000004.10:164254214::GT	NC_000004.12:163113607:TGTGT:TGTGT… NC_000004.12:163113607:TGTGT:TGTGTGT	(self)
24259046, 13494101, 9585110, 958516, 5977966, 5097060, 27027648, 13494101, ss498934899, ss663476333, ss666286834, ss980926269, ss1373063828, ss1536438373, ss1576388397, ss1704447385, ss1704448212, ss1802518341, ss1969929639, ss2030645480, ss2625830849, ss2817929980, ss2995932289, ss3644170593, ss3663846862, ss3731812195, ss3784928690, ss3790355327, ss3795230955, ss3828928599, ss3837915960, ss5169058341, ss5507819085, ss5636570821, ss5845036239, ss5964980492	NC_000004.11:164034759::TG	NC_000004.12:163113607:TGTGT:TGTGT… NC_000004.12:163113607:TGTGT:TGTGTGT	(self)
ss557572718	NC_000004.11:164034764::GT	NC_000004.12:163113607:TGTGT:TGTGT… NC_000004.12:163113607:TGTGT:TGTGTGT	(self)
31902040, 11934630, 38177748, ss3065001116, ss3645840383, ss3713516130, ss3805855686, ss3843356936, ss3955556629, ss5261838700, ss5460307964, ss5544376105, ss5704340644, ss5805741489, ss5854543968, ss5866436433	NC_000004.12:163113607::TG	NC_000004.12:163113607:TGTGT:TGTGT… NC_000004.12:163113607:TGTGT:TGTGTGT	(self)
935462061	NC_000004.12:163113607:TGTGT:TGTGT… NC_000004.12:163113607:TGTGT:TGTGTGT	NC_000004.12:163113607:TGTGT:TGTGT… NC_000004.12:163113607:TGTGT:TGTGTGT	(self)
ss154921674	NT_016354.19:88582480::TG	NC_000004.12:163113607:TGTGT:TGTGT… NC_000004.12:163113607:TGTGT:TGTGTGT	(self)
ss81702582, ss81849911, ss103883656, ss154921682, ss287761430	NT_016354.19:88582485::GT	NC_000004.12:163113607:TGTGT:TGTGT… NC_000004.12:163113607:TGTGT:TGTGTGT	(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 rs74353715

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

rs74353715