Name: rs111401943
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.

rs111401943

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr4:86881679-86881690 (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: delTT / delT / dupT / dupTT
Variation Type: Indel Insertion and Deletion
Frequency: dupT=0.04803 (713/14844, ALFA)
dupT=0.1817 (910/5008, 1000G)
dupT=0.1907 (735/3854, ALSPAC) (+ 3 more)
dupT=0.1793 (665/3708, TWINSUK)
dupT=0.2096 (384/1832, Korea1K)
dupT=0.140 (84/600, NorthernSweden)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: C4orf36 : 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	14844	TTTTTTTTTTTT=0.95197	TTTTTTTTTT=0.00000, TTTTTTTTTTT=0.00000, TTTTTTTTTTTTT=0.04803, TTTTTTTTTTTTTT=0.00000	0.912557	0.008623	0.07882	32
European	Sub	11520	TTTTTTTTTTTT=0.93828	TTTTTTTTTT=0.00000, TTTTTTTTTTT=0.00000, TTTTTTTTTTTTT=0.06172, TTTTTTTTTTTTTT=0.00000	0.8875	0.010937	0.101562	32
African	Sub	2348	TTTTTTTTTTTT=1.0000	TTTTTTTTTT=0.0000, TTTTTTTTTTT=0.0000, TTTTTTTTTTTTT=0.0000, TTTTTTTTTTTTTT=0.0000	1.0	0.0	0.0	N/A
African Others	Sub	104	TTTTTTTTTTTT=1.000	TTTTTTTTTT=0.000, TTTTTTTTTTT=0.000, TTTTTTTTTTTTT=0.000, TTTTTTTTTTTTTT=0.000	1.0	0.0	0.0	N/A
African American	Sub	2244	TTTTTTTTTTTT=1.0000	TTTTTTTTTT=0.0000, TTTTTTTTTTT=0.0000, TTTTTTTTTTTTT=0.0000, TTTTTTTTTTTTTT=0.0000	1.0	0.0	0.0	N/A
Asian	Sub	80	TTTTTTTTTTTT=1.00	TTTTTTTTTT=0.00, TTTTTTTTTTT=0.00, TTTTTTTTTTTTT=0.00, TTTTTTTTTTTTTT=0.00	1.0	0.0	0.0	N/A
East Asian	Sub	62	TTTTTTTTTTTT=1.00	TTTTTTTTTT=0.00, TTTTTTTTTTT=0.00, TTTTTTTTTTTTT=0.00, TTTTTTTTTTTTTT=0.00	1.0	0.0	0.0	N/A
Other Asian	Sub	18	TTTTTTTTTTTT=1.00	TTTTTTTTTT=0.00, TTTTTTTTTTT=0.00, TTTTTTTTTTTTT=0.00, TTTTTTTTTTTTTT=0.00	1.0	0.0	0.0	N/A
Latin American 1	Sub	100	TTTTTTTTTTTT=1.00	TTTTTTTTTT=0.00, TTTTTTTTTTT=0.00, TTTTTTTTTTTTT=0.00, TTTTTTTTTTTTTT=0.00	1.0	0.0	0.0	N/A
Latin American 2	Sub	392	TTTTTTTTTTTT=1.000	TTTTTTTTTT=0.000, TTTTTTTTTTT=0.000, TTTTTTTTTTTTT=0.000, TTTTTTTTTTTTTT=0.000	1.0	0.0	0.0	N/A
South Asian	Sub	56	TTTTTTTTTTTT=1.00	TTTTTTTTTT=0.00, TTTTTTTTTTT=0.00, TTTTTTTTTTTTT=0.00, TTTTTTTTTTTTTT=0.00	1.0	0.0	0.0	N/A
Other	Sub	348	TTTTTTTTTTTT=0.994	TTTTTTTTTT=0.000, TTTTTTTTTTT=0.000, TTTTTTTTTTTTT=0.006, TTTTTTTTTTTTTT=0.000	0.994253	0.005747	0.0	32

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").

Download

Study	Population	Group	Sample Size	Ref Allele	Alt Allele
Allele Frequency Aggregator	Total	Global	14844	(T)₁₂=0.95197	delTT=0.00000, delT=0.00000, dupT=0.04803, dupTT=0.00000
Allele Frequency Aggregator	European	Sub	11520	(T)₁₂=0.93828	delTT=0.00000, delT=0.00000, dupT=0.06172, dupTT=0.00000
Allele Frequency Aggregator	African	Sub	2348	(T)₁₂=1.0000	delTT=0.0000, delT=0.0000, dupT=0.0000, dupTT=0.0000
Allele Frequency Aggregator	Latin American 2	Sub	392	(T)₁₂=1.000	delTT=0.000, delT=0.000, dupT=0.000, dupTT=0.000
Allele Frequency Aggregator	Other	Sub	348	(T)₁₂=0.994	delTT=0.000, delT=0.000, dupT=0.006, dupTT=0.000
Allele Frequency Aggregator	Latin American 1	Sub	100	(T)₁₂=1.00	delTT=0.00, delT=0.00, dupT=0.00, dupTT=0.00
Allele Frequency Aggregator	Asian	Sub	80	(T)₁₂=1.00	delTT=0.00, delT=0.00, dupT=0.00, dupTT=0.00
Allele Frequency Aggregator	South Asian	Sub	56	(T)₁₂=1.00	delTT=0.00, delT=0.00, dupT=0.00, dupTT=0.00
1000Genomes	Global	Study-wide	5008	- No frequency provided	dupT=0.1817
1000Genomes	African	Sub	1322	- No frequency provided	dupT=0.0983
1000Genomes	East Asian	Sub	1008	- No frequency provided	dupT=0.1905
1000Genomes	Europe	Sub	1006	- No frequency provided	dupT=0.2038
1000Genomes	South Asian	Sub	978	- No frequency provided	dupT=0.240
1000Genomes	American	Sub	694	- No frequency provided	dupT=0.213
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	- No frequency provided	dupT=0.1907
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	- No frequency provided	dupT=0.1793
Korean Genome Project	KOREAN	Study-wide	1832	- No frequency provided	dupT=0.2096
Northern Sweden	ACPOP	Study-wide	600	- No frequency provided	dupT=0.140

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.86881689_86881690del
GRCh38.p14 chr 4	NC_000004.12:g.86881690del
GRCh38.p14 chr 4	NC_000004.12:g.86881690dup
GRCh38.p14 chr 4	NC_000004.12:g.86881689_86881690dup
GRCh37.p13 chr 4	NC_000004.11:g.87802842_87802843del
GRCh37.p13 chr 4	NC_000004.11:g.87802843del
GRCh37.p13 chr 4	NC_000004.11:g.87802843dup
GRCh37.p13 chr 4	NC_000004.11:g.87802842_87802843dup

Gene: C4orf36, chromosome 4 open reading frame 36 (minus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
C4orf36 transcript variant 1	NM_144645.4:c.3-5237_3-… NM_144645.4:c.3-5237_3-5236del	N/A	Intron Variant
C4orf36 transcript variant 2	NM_001369888.1:c.	N/A	Genic Downstream Transcript Variant
C4orf36 transcript variant 3	NM_001369889.1:c.	N/A	Genic Downstream Transcript Variant
C4orf36 transcript variant X1	XM_011531612.4:c.	N/A	Genic Downstream Transcript Variant
C4orf36 transcript variant X3	XM_011531613.4:c.	N/A	Genic Downstream Transcript Variant
C4orf36 transcript variant X4	XM_011531615.4:c.	N/A	Genic Downstream Transcript Variant
C4orf36 transcript variant X2	XM_017007746.3: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)₁₂=	delTT	delT	dupT	dupTT
GRCh38.p14 chr 4	NC_000004.12:g.86881679_86881690=	NC_000004.12:g.86881689_86881690del	NC_000004.12:g.86881690del	NC_000004.12:g.86881690dup	NC_000004.12:g.86881689_86881690dup
GRCh37.p13 chr 4	NC_000004.11:g.87802832_87802843=	NC_000004.11:g.87802842_87802843del	NC_000004.11:g.87802843del	NC_000004.11:g.87802843dup	NC_000004.11:g.87802842_87802843dup
C4orf36 transcript	NM_144645.3:c.*3-5236=	NM_144645.3:c.3-5237_3-5236del	NM_144645.3:c.*3-5236del	NM_144645.3:c.*3-5236dup	NM_144645.3:c.3-5237_3-5236dup
C4orf36 transcript variant 1	NM_144645.4:c.*3-5236=	NM_144645.4:c.3-5237_3-5236del	NM_144645.4:c.*3-5236del	NM_144645.4:c.*3-5236dup	NM_144645.4:c.3-5237_3-5236dup

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#.

36 SubSNP, 14 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	BUSHMAN	ss193748074	Jul 04, 2010 (132)
2	GMI	ss288551898	May 04, 2012 (138)
3	SSMP	ss663535694	Apr 01, 2015 (144)
4	1000GENOMES	ss1372431873	Aug 21, 2014 (142)
5	EVA_UK10K_ALSPAC	ss1704244518	Apr 01, 2015 (144)
6	EVA_UK10K_TWINSUK	ss1704244731	Apr 01, 2015 (144)
7	JJLAB	ss2030612020	Sep 14, 2016 (149)
8	SWEGEN	ss2995067178	Nov 08, 2017 (151)
9	MCHAISSO	ss3064978739	Nov 08, 2017 (151)
10	EVA_DECODE	ss3712485836	Jul 13, 2019 (153)
11	EVA_DECODE	ss3712485837	Jul 13, 2019 (153)
12	EVA_DECODE	ss3712485838	Jul 13, 2019 (153)
13	ACPOP	ss3731345555	Jul 13, 2019 (153)
14	PACBIO	ss3784779996	Jul 13, 2019 (153)
15	PACBIO	ss3790228336	Jul 13, 2019 (153)
16	PACBIO	ss3795103698	Jul 13, 2019 (153)
17	KHV_HUMAN_GENOMES	ss3805211709	Jul 13, 2019 (153)
18	EVA	ss3828658619	Apr 26, 2020 (154)
19	KOGIC	ss3954587209	Apr 26, 2020 (154)
20	GNOMAD	ss4115186055	Apr 26, 2021 (155)
21	GNOMAD	ss4115186056	Apr 26, 2021 (155)
22	GNOMAD	ss4115186057	Apr 26, 2021 (155)
23	GNOMAD	ss4115186058	Apr 26, 2021 (155)
24	TOMMO_GENOMICS	ss5166698310	Apr 26, 2021 (155)
25	TOMMO_GENOMICS	ss5166698311	Apr 26, 2021 (155)
26	1000G_HIGH_COVERAGE	ss5259982648	Oct 17, 2022 (156)
27	1000G_HIGH_COVERAGE	ss5259982649	Oct 17, 2022 (156)
28	1000G_HIGH_COVERAGE	ss5259982650	Oct 17, 2022 (156)
29	HUGCELL_USP	ss5458657763	Oct 17, 2022 (156)
30	EVA	ss5507605014	Oct 17, 2022 (156)
31	TOMMO_GENOMICS	ss5701320817	Oct 17, 2022 (156)
32	TOMMO_GENOMICS	ss5701320818	Oct 17, 2022 (156)
33	YY_MCH	ss5805280322	Oct 17, 2022 (156)
34	EVA	ss5844301816	Oct 17, 2022 (156)
35	EVA	ss5854319710	Oct 17, 2022 (156)
36	EVA	ss5963873161	Oct 17, 2022 (156)
37	1000Genomes	NC_000004.11 - 87802832	Oct 12, 2018 (152)
38	The Avon Longitudinal Study of Parents and Children	NC_000004.11 - 87802832	Oct 12, 2018 (152)
39	gnomAD - Genomes Submission ignored due to conflicting rows: Row 156262042 (NC_000004.12:86881678::T 22085/134536) Row 156262043 (NC_000004.12:86881678::TT 8/134696) Row 156262044 (NC_000004.12:86881678:T: 73/134498)...	-	Apr 26, 2021 (155)
40	gnomAD - Genomes Submission ignored due to conflicting rows: Row 156262042 (NC_000004.12:86881678::T 22085/134536) Row 156262043 (NC_000004.12:86881678::TT 8/134696) Row 156262044 (NC_000004.12:86881678:T: 73/134498)...	-	Apr 26, 2021 (155)
41	gnomAD - Genomes Submission ignored due to conflicting rows: Row 156262042 (NC_000004.12:86881678::T 22085/134536) Row 156262043 (NC_000004.12:86881678::TT 8/134696) Row 156262044 (NC_000004.12:86881678:T: 73/134498)...	-	Apr 26, 2021 (155)
42	gnomAD - Genomes Submission ignored due to conflicting rows: Row 156262042 (NC_000004.12:86881678::T 22085/134536) Row 156262043 (NC_000004.12:86881678::TT 8/134696) Row 156262044 (NC_000004.12:86881678:T: 73/134498)...	-	Apr 26, 2021 (155)
43	Korean Genome Project	NC_000004.12 - 86881679	Apr 26, 2020 (154)
44	Northern Sweden	NC_000004.11 - 87802832	Jul 13, 2019 (153)
45	8.3KJPN Submission ignored due to conflicting rows: Row 24667617 (NC_000004.11:87802831::T 3141/16760) Row 24667618 (NC_000004.11:87802831:T: 2/16760)	-	Apr 26, 2021 (155)
46	8.3KJPN Submission ignored due to conflicting rows: Row 24667617 (NC_000004.11:87802831::T 3141/16760) Row 24667618 (NC_000004.11:87802831:T: 2/16760)	-	Apr 26, 2021 (155)
47	14KJPN Submission ignored due to conflicting rows: Row 35157921 (NC_000004.12:86881678::T 5316/28258) Row 35157922 (NC_000004.12:86881678:T: 4/28258)	-	Oct 17, 2022 (156)
48	14KJPN Submission ignored due to conflicting rows: Row 35157921 (NC_000004.12:86881678::T 5316/28258) Row 35157922 (NC_000004.12:86881678:T: 4/28258)	-	Oct 17, 2022 (156)
49	UK 10K study - Twins	NC_000004.11 - 87802832	Oct 12, 2018 (152)
50	ALFA	NC_000004.12 - 86881679	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)
rs199574351	May 15, 2013 (138)
rs368644357	May 15, 2013 (138)
rs1047259223	Nov 08, 2017 (151)

Added to this RefSNP Cluster:

Submission IDs	Observation SPDI	Canonical SPDI	Source RSIDs
ss4115186058	NC_000004.12:86881678:TT:	NC_000004.12:86881678:TTTTTTTTTTTT… NC_000004.12:86881678:TTTTTTTTTTTT:TTTTTTTTTT	(self)
2815619587	NC_000004.12:86881678:TTTTTTTTTTTT… NC_000004.12:86881678:TTTTTTTTTTTT:TTTTTTTTTT	NC_000004.12:86881678:TTTTTTTTTTTT… NC_000004.12:86881678:TTTTTTTTTTTT:TTTTTTTTTT	(self)
ss5166698311, ss5507605014	NC_000004.11:87802831:T:	NC_000004.12:86881678:TTTTTTTTTTTT… NC_000004.12:86881678:TTTTTTTTTTTT:TTTTTTTTTTT	(self)
ss3712485836, ss4115186057, ss5259982650, ss5701320818	NC_000004.12:86881678:T:	NC_000004.12:86881678:TTTTTTTTTTTT… NC_000004.12:86881678:TTTTTTTTTTTT:TTTTTTTTTTT	(self)
2815619587	NC_000004.12:86881678:TTTTTTTTTTTT… NC_000004.12:86881678:TTTTTTTTTTTT:TTTTTTTTTTT	NC_000004.12:86881678:TTTTTTTTTTTT… NC_000004.12:86881678:TTTTTTTTTTTT:TTTTTTTTTTT	(self)
ss288551898	NC_000004.10:88021867::T	NC_000004.12:86881678:TTTTTTTTTTTT… NC_000004.12:86881678:TTTTTTTTTTTT:TTTTTTTTTTTTT	(self)
22061297, 12270341, 4630420, 12270341, ss663535694, ss1372431873, ss1704244518, ss1704244731, ss2030612020, ss2995067178, ss3731345555, ss3784779996, ss3790228336, ss3795103698, ss3828658619, ss5166698310, ss5844301816, ss5963873161	NC_000004.11:87802831::T	NC_000004.12:86881678:TTTTTTTTTTTT… NC_000004.12:86881678:TTTTTTTTTTTT:TTTTTTTTTTTTT	(self)
10965210, ss3064978739, ss3805211709, ss3954587209, ss4115186055, ss5259982648, ss5458657763, ss5701320817, ss5805280322, ss5854319710	NC_000004.12:86881678::T	NC_000004.12:86881678:TTTTTTTTTTTT… NC_000004.12:86881678:TTTTTTTTTTTT:TTTTTTTTTTTTT	(self)
2815619587	NC_000004.12:86881678:TTTTTTTTTTTT… NC_000004.12:86881678:TTTTTTTTTTTT:TTTTTTTTTTTTT	NC_000004.12:86881678:TTTTTTTTTTTT… NC_000004.12:86881678:TTTTTTTTTTTT:TTTTTTTTTTTTT	(self)
ss3712485837	NC_000004.12:86881679::T	NC_000004.12:86881678:TTTTTTTTTTTT… NC_000004.12:86881678:TTTTTTTTTTTT:TTTTTTTTTTTTT	(self)
ss193748074	NT_016354.20:27960297::T	NC_000004.12:86881678:TTTTTTTTTTTT… NC_000004.12:86881678:TTTTTTTTTTTT:TTTTTTTTTTTTT	(self)
ss4115186056, ss5259982649	NC_000004.12:86881678::TT	NC_000004.12:86881678:TTTTTTTTTTTT… NC_000004.12:86881678:TTTTTTTTTTTT:TTTTTTTTTTTTTT	(self)
2815619587	NC_000004.12:86881678:TTTTTTTTTTTT… NC_000004.12:86881678:TTTTTTTTTTTT:TTTTTTTTTTTTTT	NC_000004.12:86881678:TTTTTTTTTTTT… NC_000004.12:86881678:TTTTTTTTTTTT:TTTTTTTTTTTTTT	(self)
ss3712485838	NC_000004.12:86881679::TT	NC_000004.12:86881678:TTTTTTTTTTTT… NC_000004.12:86881678:TTTTTTTTTTTT:TTTTTTTTTTTTTT	(self)

Removed from this RefSNP Cluster:

Submission IDs	Observation SPDI	Canonical SPDI	Destination RSIDs
ss2432492180	NC_000004.11:87802831:TT:	NC_000004.12:86881678:TTTTTTTTTTTT… NC_000004.12:86881678:TTTTTTTTTTTT:TTTTTTTTTT

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

No publications for rs111401943

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.

Choose placement

dbSNP Short Genetic Variations

Welcome to the Reference SNP (rs) Report

Reference SNP (rs) Report

rs111401943