Name: rs368894000
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.

rs368894000

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr19:36075041-36075051 (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
Variation Type: Indel Insertion and Deletion
Frequency: dupT=0.00005 (1/18338, ALFA)
dupT=0.00179 (30/16760, 8.3KJPN)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: WDR62 : 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	HTRZ	HWEP
Total	Global	18338	TTTTTTTTTTT=0.99995	TTTTTTTTT=0.00000, TTTTTTTTTT=0.00000, TTTTTTTTTTTT=0.00005	0.999891	0.000109	0
European	Sub	14146	TTTTTTTTTTT=0.99993	TTTTTTTTT=0.00000, TTTTTTTTTT=0.00000, TTTTTTTTTTTT=0.00007	0.999859	0.000141	0
African	Sub	2748	TTTTTTTTTTT=1.0000	TTTTTTTTT=0.0000, TTTTTTTTTT=0.0000, TTTTTTTTTTTT=0.0000	1.0	0.0	N/A
African Others	Sub	106	TTTTTTTTTTT=1.000	TTTTTTTTT=0.000, TTTTTTTTTT=0.000, TTTTTTTTTTTT=0.000	1.0	0.0	N/A
African American	Sub	2642	TTTTTTTTTTT=1.0000	TTTTTTTTT=0.0000, TTTTTTTTTT=0.0000, TTTTTTTTTTTT=0.0000	1.0	0.0	N/A
Asian	Sub	112	TTTTTTTTTTT=1.000	TTTTTTTTT=0.000, TTTTTTTTTT=0.000, TTTTTTTTTTTT=0.000	1.0	0.0	N/A
East Asian	Sub	86	TTTTTTTTTTT=1.00	TTTTTTTTT=0.00, TTTTTTTTTT=0.00, TTTTTTTTTTTT=0.00	1.0	0.0	N/A
Other Asian	Sub	26	TTTTTTTTTTT=1.00	TTTTTTTTT=0.00, TTTTTTTTTT=0.00, TTTTTTTTTTTT=0.00	1.0	0.0	N/A
Latin American 1	Sub	144	TTTTTTTTTTT=1.000	TTTTTTTTT=0.000, TTTTTTTTTT=0.000, TTTTTTTTTTTT=0.000	1.0	0.0	N/A
Latin American 2	Sub	598	TTTTTTTTTTT=1.000	TTTTTTTTT=0.000, TTTTTTTTTT=0.000, TTTTTTTTTTTT=0.000	1.0	0.0	N/A
South Asian	Sub	98	TTTTTTTTTTT=1.00	TTTTTTTTT=0.00, TTTTTTTTTT=0.00, TTTTTTTTTTTT=0.00	1.0	0.0	N/A
Other	Sub	492	TTTTTTTTTTT=1.000	TTTTTTTTT=0.000, TTTTTTTTTT=0.000, TTTTTTTTTTTT=0.000	1.0	0.0	N/A

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
Allele Frequency Aggregator	Total	Global	18338	(T)₁₁=0.99995	delTT=0.00000, delT=0.00000, dupT=0.00005
Allele Frequency Aggregator	European	Sub	14146	(T)₁₁=0.99993	delTT=0.00000, delT=0.00000, dupT=0.00007
Allele Frequency Aggregator	African	Sub	2748	(T)₁₁=1.0000	delTT=0.0000, delT=0.0000, dupT=0.0000
Allele Frequency Aggregator	Latin American 2	Sub	598	(T)₁₁=1.000	delTT=0.000, delT=0.000, dupT=0.000
Allele Frequency Aggregator	Other	Sub	492	(T)₁₁=1.000	delTT=0.000, delT=0.000, dupT=0.000
Allele Frequency Aggregator	Latin American 1	Sub	144	(T)₁₁=1.000	delTT=0.000, delT=0.000, dupT=0.000
Allele Frequency Aggregator	Asian	Sub	112	(T)₁₁=1.000	delTT=0.000, delT=0.000, dupT=0.000
Allele Frequency Aggregator	South Asian	Sub	98	(T)₁₁=1.00	delTT=0.00, delT=0.00, dupT=0.00
8.3KJPN	JAPANESE	Study-wide	16760	- No frequency provided	dupT=0.00179

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 19	NC_000019.10:g.36075050_36075051del
GRCh38.p14 chr 19	NC_000019.10:g.36075051del
GRCh38.p14 chr 19	NC_000019.10:g.36075051dup
GRCh37.p13 chr 19	NC_000019.9:g.36565952_36565953del
GRCh37.p13 chr 19	NC_000019.9:g.36565953del
GRCh37.p13 chr 19	NC_000019.9:g.36565953dup
WDR62 RefSeqGene	NG_028101.1:g.25170_25171del
WDR62 RefSeqGene	NG_028101.1:g.25171del
WDR62 RefSeqGene	NG_028101.1:g.25171dup

Gene: WDR62, WD repeat domain 62 (plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
WDR62 transcript variant 1	NM_001083961.2:c.1233+151… NM_001083961.2:c.1233+1519_1233+1520del	N/A	Intron Variant
WDR62 transcript variant 2	NM_173636.5:c.1233+1519_1… NM_173636.5:c.1233+1519_1233+1520del	N/A	Intron Variant
WDR62 transcript variant X3	XM_005258809.3:c.1233+151… XM_005258809.3:c.1233+1519_1233+1520del	N/A	Intron Variant
WDR62 transcript variant X2	XM_011526837.2:c.1218+151… XM_011526837.2:c.1218+1519_1218+1520del	N/A	Intron Variant
WDR62 transcript variant X8	XM_011526838.2:c.1233+151… XM_011526838.2:c.1233+1519_1233+1520del	N/A	Intron Variant
WDR62 transcript variant X10	XM_011526839.2:c.883-6383… XM_011526839.2:c.883-6383_883-6382del	N/A	Intron Variant
WDR62 transcript variant X12	XM_011526840.3:c.75-790_7… XM_011526840.3:c.75-790_75-789del	N/A	Intron Variant
WDR62 transcript variant X1	XM_017026665.2:c.1233+151… XM_017026665.2:c.1233+1519_1233+1520del	N/A	Intron Variant
WDR62 transcript variant X2	XM_047438657.1:c.1218+151… XM_047438657.1:c.1218+1519_1218+1520del	N/A	Intron Variant
WDR62 transcript variant X4	XM_047438658.1:c.1233+151… XM_047438658.1:c.1233+1519_1233+1520del	N/A	Intron Variant
WDR62 transcript variant X5	XM_047438659.1:c.1218+151… XM_047438659.1:c.1218+1519_1218+1520del	N/A	Intron Variant
WDR62 transcript variant X6	XM_047438660.1:c.1218+151… XM_047438660.1:c.1218+1519_1218+1520del	N/A	Intron Variant
WDR62 transcript variant X7	XM_047438661.1:c.1218+151… XM_047438661.1:c.1218+1519_1218+1520del	N/A	Intron Variant
WDR62 transcript variant X8	XM_047438662.1:c.883-6383… XM_047438662.1:c.883-6383_883-6382del	N/A	Intron Variant
WDR62 transcript variant X9	XM_047438663.1:c.883-6383… XM_047438663.1:c.883-6383_883-6382del	N/A	Intron Variant
WDR62 transcript variant X10	XM_047438664.1:c.883-6383… XM_047438664.1:c.883-6383_883-6382del	N/A	Intron Variant
WDR62 transcript variant X11	XM_047438665.1:c.883-6383… XM_047438665.1:c.883-6383_883-6382del	N/A	Intron Variant
WDR62 transcript variant X13	XM_047438666.1:c.75-790_7… XM_047438666.1:c.75-790_75-789del	N/A	Intron Variant
WDR62 transcript variant X14	XM_011526841.3:c.	N/A	Genic Upstream Transcript Variant
WDR62 transcript variant X15	XM_011526842.2:c.	N/A	Genic Upstream Transcript Variant
WDR62 transcript variant X16	XM_011526843.2:c.	N/A	Genic Upstream Transcript Variant
WDR62 transcript variant X17	XM_011526844.3:c.	N/A	Genic Upstream Transcript Variant
WDR62 transcript variant X18	XR_001753671.2:n.	N/A	Intron Variant
WDR62 transcript variant X19	XR_001753672.2: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	(T)₁₁=	delTT	delT	dupT
GRCh38.p14 chr 19	NC_000019.10:g.36075041_36075051=	NC_000019.10:g.36075050_36075051del	NC_000019.10:g.36075051del	NC_000019.10:g.36075051dup
GRCh37.p13 chr 19	NC_000019.9:g.36565943_36565953=	NC_000019.9:g.36565952_36565953del	NC_000019.9:g.36565953del	NC_000019.9:g.36565953dup
WDR62 RefSeqGene	NG_028101.1:g.25161_25171=	NG_028101.1:g.25170_25171del	NG_028101.1:g.25171del	NG_028101.1:g.25171dup
WDR62 transcript variant 1	NM_001083961.1:c.1233+1510=	NM_001083961.1:c.1233+1519_1233+1520del	NM_001083961.1:c.1233+1520del	NM_001083961.1:c.1233+1520dup
WDR62 transcript variant 1	NM_001083961.2:c.1233+1510=	NM_001083961.2:c.1233+1519_1233+1520del	NM_001083961.2:c.1233+1520del	NM_001083961.2:c.1233+1520dup
WDR62 transcript variant 2	NM_173636.4:c.1233+1510=	NM_173636.4:c.1233+1519_1233+1520del	NM_173636.4:c.1233+1520del	NM_173636.4:c.1233+1520dup
WDR62 transcript variant 2	NM_173636.5:c.1233+1510=	NM_173636.5:c.1233+1519_1233+1520del	NM_173636.5:c.1233+1520del	NM_173636.5:c.1233+1520dup
WDR62 transcript variant X1	XM_005258809.1:c.1233+1510=	XM_005258809.1:c.1233+1519_1233+1520del	XM_005258809.1:c.1233+1520del	XM_005258809.1:c.1233+1520dup
WDR62 transcript variant X3	XM_005258809.3:c.1233+1510=	XM_005258809.3:c.1233+1519_1233+1520del	XM_005258809.3:c.1233+1520del	XM_005258809.3:c.1233+1520dup
WDR62 transcript variant X2	XM_011526837.2:c.1218+1510=	XM_011526837.2:c.1218+1519_1218+1520del	XM_011526837.2:c.1218+1520del	XM_011526837.2:c.1218+1520dup
WDR62 transcript variant X8	XM_011526838.2:c.1233+1510=	XM_011526838.2:c.1233+1519_1233+1520del	XM_011526838.2:c.1233+1520del	XM_011526838.2:c.1233+1520dup
WDR62 transcript variant X10	XM_011526839.2:c.883-6392=	XM_011526839.2:c.883-6383_883-6382del	XM_011526839.2:c.883-6382del	XM_011526839.2:c.883-6382dup
WDR62 transcript variant X12	XM_011526840.3:c.75-799=	XM_011526840.3:c.75-790_75-789del	XM_011526840.3:c.75-789del	XM_011526840.3:c.75-789dup
WDR62 transcript variant X1	XM_017026665.2:c.1233+1510=	XM_017026665.2:c.1233+1519_1233+1520del	XM_017026665.2:c.1233+1520del	XM_017026665.2:c.1233+1520dup
WDR62 transcript variant X2	XM_047438657.1:c.1218+1510=	XM_047438657.1:c.1218+1519_1218+1520del	XM_047438657.1:c.1218+1520del	XM_047438657.1:c.1218+1520dup
WDR62 transcript variant X4	XM_047438658.1:c.1233+1510=	XM_047438658.1:c.1233+1519_1233+1520del	XM_047438658.1:c.1233+1520del	XM_047438658.1:c.1233+1520dup
WDR62 transcript variant X5	XM_047438659.1:c.1218+1510=	XM_047438659.1:c.1218+1519_1218+1520del	XM_047438659.1:c.1218+1520del	XM_047438659.1:c.1218+1520dup
WDR62 transcript variant X6	XM_047438660.1:c.1218+1510=	XM_047438660.1:c.1218+1519_1218+1520del	XM_047438660.1:c.1218+1520del	XM_047438660.1:c.1218+1520dup
WDR62 transcript variant X7	XM_047438661.1:c.1218+1510=	XM_047438661.1:c.1218+1519_1218+1520del	XM_047438661.1:c.1218+1520del	XM_047438661.1:c.1218+1520dup
WDR62 transcript variant X8	XM_047438662.1:c.883-6392=	XM_047438662.1:c.883-6383_883-6382del	XM_047438662.1:c.883-6382del	XM_047438662.1:c.883-6382dup
WDR62 transcript variant X9	XM_047438663.1:c.883-6392=	XM_047438663.1:c.883-6383_883-6382del	XM_047438663.1:c.883-6382del	XM_047438663.1:c.883-6382dup
WDR62 transcript variant X10	XM_047438664.1:c.883-6392=	XM_047438664.1:c.883-6383_883-6382del	XM_047438664.1:c.883-6382del	XM_047438664.1:c.883-6382dup
WDR62 transcript variant X11	XM_047438665.1:c.883-6392=	XM_047438665.1:c.883-6383_883-6382del	XM_047438665.1:c.883-6382del	XM_047438665.1:c.883-6382dup
WDR62 transcript variant X13	XM_047438666.1:c.75-799=	XM_047438666.1:c.75-790_75-789del	XM_047438666.1:c.75-789del	XM_047438666.1:c.75-789dup

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#.

15 SubSNP, 9 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	TISHKOFF	ss565673414	Apr 25, 2013 (138)
2	HAMMER_LAB	ss1809295948	Sep 08, 2015 (146)
3	SWEGEN	ss3017425720	Nov 08, 2017 (151)
4	GNOMAD	ss4330772712	Apr 26, 2021 (155)
5	GNOMAD	ss4330772713	Apr 26, 2021 (155)
6	GNOMAD	ss4330772714	Apr 26, 2021 (155)
7	TOPMED	ss5073956261	Apr 26, 2021 (155)
8	TOPMED	ss5073956262	Apr 26, 2021 (155)
9	TOMMO_GENOMICS	ss5227624222	Apr 26, 2021 (155)
10	1000G_HIGH_COVERAGE	ss5307153728	Oct 16, 2022 (156)
11	1000G_HIGH_COVERAGE	ss5307153729	Oct 16, 2022 (156)
12	HUGCELL_USP	ss5499692604	Oct 16, 2022 (156)
13	HUGCELL_USP	ss5499692605	Oct 16, 2022 (156)
14	TOMMO_GENOMICS	ss5786213423	Oct 16, 2022 (156)
15	TOMMO_GENOMICS	ss5786213424	Oct 16, 2022 (156)
16	gnomAD - Genomes Submission ignored due to conflicting rows: Row 539290019 (NC_000019.10:36075040::T 1153/134694) Row 539290020 (NC_000019.10:36075040:T: 41/134800) Row 539290021 (NC_000019.10:36075040:TT: 1/134838)	-	Apr 26, 2021 (155)
17	gnomAD - Genomes Submission ignored due to conflicting rows: Row 539290019 (NC_000019.10:36075040::T 1153/134694) Row 539290020 (NC_000019.10:36075040:T: 41/134800) Row 539290021 (NC_000019.10:36075040:TT: 1/134838)	-	Apr 26, 2021 (155)
18	gnomAD - Genomes Submission ignored due to conflicting rows: Row 539290019 (NC_000019.10:36075040::T 1153/134694) Row 539290020 (NC_000019.10:36075040:T: 41/134800) Row 539290021 (NC_000019.10:36075040:TT: 1/134838)	-	Apr 26, 2021 (155)
19	8.3KJPN	NC_000019.9 - 36565943	Apr 26, 2021 (155)
20	14KJPN Submission ignored due to conflicting rows: Row 120050527 (NC_000019.10:36075040:T: 10/28258) Row 120050528 (NC_000019.10:36075040::T 43/28258)	-	Oct 16, 2022 (156)
21	14KJPN Submission ignored due to conflicting rows: Row 120050527 (NC_000019.10:36075040:T: 10/28258) Row 120050528 (NC_000019.10:36075040::T 43/28258)	-	Oct 16, 2022 (156)
22	TopMed Submission ignored due to conflicting rows: Row 289501925 (NC_000019.10:36075040:T: 118/264690) Row 289501926 (NC_000019.10:36075040:TT: 3/264690)	-	Apr 26, 2021 (155)
23	TopMed Submission ignored due to conflicting rows: Row 289501925 (NC_000019.10:36075040:T: 118/264690) Row 289501926 (NC_000019.10:36075040:TT: 3/264690)	-	Apr 26, 2021 (155)
24	ALFA	NC_000019.10 - 36075041	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).

Added to this RefSNP Cluster:

Submission IDs	Observation SPDI	Canonical SPDI	Source RSIDs
ss4330772714, ss5073956262	NC_000019.10:36075040:TT:	NC_000019.10:36075040:TTTTTTTTTTT:… NC_000019.10:36075040:TTTTTTTTTTT:TTTTTTTTT	(self)
7644789108	NC_000019.10:36075040:TTTTTTTTTTT:… NC_000019.10:36075040:TTTTTTTTTTT:TTTTTTTTT	NC_000019.10:36075040:TTTTTTTTTTT:… NC_000019.10:36075040:TTTTTTTTTTT:TTTTTTTTT	(self)
ss4330772713, ss5073956261, ss5307153729, ss5499692604, ss5786213423	NC_000019.10:36075040:T:	NC_000019.10:36075040:TTTTTTTTTTT:… NC_000019.10:36075040:TTTTTTTTTTT:TTTTTTTTTT	(self)
7644789108	NC_000019.10:36075040:TTTTTTTTTTT:… NC_000019.10:36075040:TTTTTTTTTTT:TTTTTTTTTT	NC_000019.10:36075040:TTTTTTTTTTT:… NC_000019.10:36075040:TTTTTTTTTTT:TTTTTTTTTT	(self)
85593529, ss1809295948, ss3017425720, ss5227624222	NC_000019.9:36565942::T	NC_000019.10:36075040:TTTTTTTTTTT:… NC_000019.10:36075040:TTTTTTTTTTT:TTTTTTTTTTTT	(self)
ss565673414	NC_000019.9:36565953::T	NC_000019.10:36075040:TTTTTTTTTTT:… NC_000019.10:36075040:TTTTTTTTTTT:TTTTTTTTTTTT	(self)
ss4330772712, ss5307153728, ss5499692605, ss5786213424	NC_000019.10:36075040::T	NC_000019.10:36075040:TTTTTTTTTTT:… NC_000019.10:36075040:TTTTTTTTTTT:TTTTTTTTTTTT	(self)
7644789108	NC_000019.10:36075040:TTTTTTTTTTT:… NC_000019.10:36075040:TTTTTTTTTTT:TTTTTTTTTTTT	NC_000019.10:36075040:TTTTTTTTTTT:… NC_000019.10:36075040:TTTTTTTTTTT:TTTTTTTTTTTT	(self)

Removed from this RefSNP Cluster:

Submission IDs	Observation SPDI	Canonical SPDI	Destination RSIDs
ss2391263044	NC_000019.9:36565942:T:	NC_000019.10:36075040:TTTTTTTTTTT:… NC_000019.10:36075040:TTTTTTTTTTT: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 rs368894000

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

rs368894000