rs201779890 RefSNP Report - dbSNP

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.

rs201779890

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr1:145927328 (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>G
Variation Type: SNV Single Nucleotide Variation
Frequency: G=0.003166 (838/264690, TOPMED)
G=0.005471 (1281/234162, GnomAD_exome)
G=0.005178 (726/140200, GnomAD) (+ 15 more)
G=0.00638 (577/90492, ExAC)
C=0.00099 (78/78700, PAGE_STUDY)
G=0.00639 (178/27874, ALFA)
G=0.00492 (64/13006, GO-ESP)
G=0.0006 (4/6404, 1000G_30x)
G=0.0008 (4/5008, 1000G)
G=0.0023 (9/3854, ALSPAC)
G=0.0032 (12/3708, TWINSUK)
G=0.005 (5/998, GoNL)
G=0.005 (3/600, NorthernSweden)
G=0.004 (2/534, MGP)
C=0.5 (1/2, SGDP_PRJ)
G=0.5 (1/2, SGDP_PRJ)
C=0.5 (1/2, Siberian)
G=0.5 (1/2, Siberian)

Clinical Significance: Reported in ClinVar
Gene : Consequence: LIX1L-AS1 : Non Coding Transcript Variant
RBM8A : Intron Variant
POLR3GL : 2KB Upstream Variant
Publications: 3 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	27874	C=0.99361	G=0.00639	0.987372	0.000144	0.012485	2
European	Sub	20346	C=0.99209	G=0.00791	0.98437	0.000197	0.015433	2
African	Sub	3540	C=0.9992	G=0.0008	0.998305	0.0	0.001695	0
African Others	Sub	122	C=1.000	G=0.000	1.0	0.0	0.0	N/A
African American	Sub	3418	C=0.9991	G=0.0009	0.998245	0.0	0.001755	0
Asian	Sub	168	C=1.000	G=0.000	1.0	0.0	0.0	N/A
East Asian	Sub	112	C=1.000	G=0.000	1.0	0.0	0.0	N/A
Other Asian	Sub	56	C=1.00	G=0.00	1.0	0.0	0.0	N/A
Latin American 1	Sub	146	C=1.000	G=0.000	1.0	0.0	0.0	N/A
Latin American 2	Sub	610	C=1.000	G=0.000	1.0	0.0	0.0	N/A
South Asian	Sub	98	C=1.00	G=0.00	1.0	0.0	0.0	N/A
Other	Sub	2966	C=0.9953	G=0.0047	0.99056	0.0	0.00944	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	C=0.996834	G=0.003166
gnomAD - Exomes	Global	Study-wide	234162	C=0.994529	G=0.005471
gnomAD - Exomes	European	Sub	125586	C=0.990572	G=0.009428
gnomAD - Exomes	Asian	Sub	46232	C=0.99976	G=0.00024
gnomAD - Exomes	American	Sub	32262	C=0.99864	G=0.00136
gnomAD - Exomes	African	Sub	14582	C=0.99952	G=0.00048
gnomAD - Exomes	Ashkenazi Jewish	Sub	9654	C=0.9992	G=0.0008
gnomAD - Exomes	Other	Sub	5846	C=0.9954	G=0.0046
gnomAD - Genomes	Global	Study-wide	140200	C=0.994822	G=0.005178
gnomAD - Genomes	European	Sub	75926	C=0.99106	G=0.00894
gnomAD - Genomes	African	Sub	42024	C=0.99950	G=0.00050
gnomAD - Genomes	American	Sub	13642	C=0.99853	G=0.00147
gnomAD - Genomes	Ashkenazi Jewish	Sub	3324	C=0.9994	G=0.0006
gnomAD - Genomes	East Asian	Sub	3132	C=1.0000	G=0.0000
gnomAD - Genomes	Other	Sub	2152	C=0.9981	G=0.0019
ExAC	Global	Study-wide	90492	C=0.99362	G=0.00638
ExAC	Europe	Sub	55692	C=0.99020	G=0.00980
ExAC	Asian	Sub	19512	C=0.99974	G=0.00026
ExAC	African	Sub	7588	C=0.9991	G=0.0009
ExAC	American	Sub	7022	C=0.9984	G=0.0016
ExAC	Other	Sub	678	C=0.988	G=0.012
The PAGE Study	Global	Study-wide	78700	C=0.00099	G=0.99901
The PAGE Study	AfricanAmerican	Sub	32514	C=0.00086	G=0.99914
The PAGE Study	Mexican	Sub	10810	C=0.00111	G=0.99889
The PAGE Study	Asian	Sub	8318	C=0.0000	G=1.0000
The PAGE Study	PuertoRican	Sub	7918	C=0.0010	G=0.9990
The PAGE Study	NativeHawaiian	Sub	4534	C=0.0018	G=0.9982
The PAGE Study	Cuban	Sub	4230	C=0.0026	G=0.9974
The PAGE Study	Dominican	Sub	3828	C=0.0003	G=0.9997
The PAGE Study	CentralAmerican	Sub	2450	C=0.0012	G=0.9988
The PAGE Study	SouthAmerican	Sub	1982	C=0.0020	G=0.9980
The PAGE Study	NativeAmerican	Sub	1260	C=0.0024	G=0.9976
The PAGE Study	SouthAsian	Sub	856	C=0.000	G=1.000
Allele Frequency Aggregator	Total	Global	27874	C=0.99361	G=0.00639
Allele Frequency Aggregator	European	Sub	20346	C=0.99209	G=0.00791
Allele Frequency Aggregator	African	Sub	3540	C=0.9992	G=0.0008
Allele Frequency Aggregator	Other	Sub	2966	C=0.9953	G=0.0047
Allele Frequency Aggregator	Latin American 2	Sub	610	C=1.000	G=0.000
Allele Frequency Aggregator	Asian	Sub	168	C=1.000	G=0.000
Allele Frequency Aggregator	Latin American 1	Sub	146	C=1.000	G=0.000
Allele Frequency Aggregator	South Asian	Sub	98	C=1.00	G=0.00
GO Exome Sequencing Project	Global	Study-wide	13006	C=0.99508	G=0.00492
GO Exome Sequencing Project	European American	Sub	8600	C=0.9930	G=0.0070
GO Exome Sequencing Project	African American	Sub	4406	C=0.9991	G=0.0009
1000Genomes_30x	Global	Study-wide	6404	C=0.9994	G=0.0006
1000Genomes_30x	African	Sub	1786	C=1.0000	G=0.0000
1000Genomes_30x	Europe	Sub	1266	C=0.9976	G=0.0024
1000Genomes_30x	South Asian	Sub	1202	C=1.0000	G=0.0000
1000Genomes_30x	East Asian	Sub	1170	C=1.0000	G=0.0000
1000Genomes_30x	American	Sub	980	C=0.999	G=0.001
1000Genomes	Global	Study-wide	5008	C=0.9992	G=0.0008
1000Genomes	African	Sub	1322	C=1.0000	G=0.0000
1000Genomes	East Asian	Sub	1008	C=1.0000	G=0.0000
1000Genomes	Europe	Sub	1006	C=0.9970	G=0.0030
1000Genomes	South Asian	Sub	978	C=1.000	G=0.000
1000Genomes	American	Sub	694	C=0.999	G=0.001
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	C=0.9977	G=0.0023
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	C=0.9968	G=0.0032
Genome of the Netherlands Release 5	Genome of the Netherlands	Study-wide	998	C=0.995	G=0.005
Northern Sweden	ACPOP	Study-wide	600	C=0.995	G=0.005
Medical Genome Project healthy controls from Spanish population	Spanish controls	Study-wide	534	C=0.996	G=0.004
SGDP_PRJ	Global	Study-wide	2	C=0.5	G=0.5
Siberian	Global	Study-wide	2	C=0.5	G=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.145927328C>G
GRCh37.p13 chr 1 fix patch HG1287_PATCH	NW_003871055.3:g.2742741C>G
RBM8A RefSeqGene (LRG_574)	NG_032654.2:g.5209G>C
LOC126805851 genomic region	NG_082175.1:g.1009C>G
GRCh37.p13 chr 1	NC_000001.10:g.145507765G>C

Gene: RBM8A, RNA binding motif protein 8A (minus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
RBM8A transcript	NM_005105.5:c.67+32G>C	N/A	Intron Variant

Gene: POLR3GL, RNA polymerase III subunit GL (plus strand) : 2KB Upstream Variant

Molecule type	Change	Amino acid[Codon]	SO Term
POLR3GL transcript variant 2	NM_001330685.2:c.	N/A	N/A
POLR3GL transcript variant 1	NM_032305.3:c.	N/A	N/A
POLR3GL transcript variant X1	XM_047432062.1:c.	N/A	Upstream Transcript Variant
POLR3GL transcript variant X2	XM_047432063.1:c.	N/A	Upstream Transcript Variant
POLR3GL transcript variant X3	XM_005277431.5:c.	N/A	N/A

Gene: LIX1L-AS1, LIX1L antisense RNA 1 (plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
LIX1L-AS1 transcript	NR_147182.1:n.381C>G	N/A	Non Coding 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.

Allele: G (allele ID: 39422 )

ClinVar Accession	Disease Names	Clinical Significance
RCV000023419.19	Radial aplasia-thrombocytopenia syndrome	Pathogenic
RCV000172898.14	not provided	Pathogenic
RCV001270062.1	Abnormality of brain morphology,Clinodactyly of the 5th finger,Global developmental delay	Likely-Pathogenic

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=	G
GRCh38.p14 chr 1	NC_000001.11:g.145927328=	NC_000001.11:g.145927328C>G
GRCh37.p13 chr 1 fix patch HG1287_PATCH	NW_003871055.3:g.2742741=	NW_003871055.3:g.2742741C>G
RBM8A RefSeqGene (LRG_574)	NG_032654.2:g.5209=	NG_032654.2:g.5209G>C
LOC126805851 genomic region	NG_082175.1:g.1009=	NG_082175.1:g.1009C>G
GRCh37.p13 chr 1	NC_000001.10:g.145507765=	NC_000001.10:g.145507765G>C
LIX1L-AS1 transcript	NR_147182.1:n.381=	NR_147182.1:n.381C>G
RBM8A transcript	NM_005105.4:c.67+32=	NM_005105.4:c.67+32G>C
RBM8A transcript	NM_005105.5:c.67+32=	NM_005105.5:c.67+32G>C
RBM8A transcript variant X1	XM_005272985.1:c.67+32=	XM_005272985.1:c.67+32G>C
RBM8A transcript variant X1	XM_005277456.1:c.67+32=	XM_005277456.1:c.67+32G>C
RBM8A transcript variant X3	XM_005277458.1:c.-179+32=	XM_005277458.1:c.-179+32G>C

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, 16 Frequency, 3 ClinVar submissions

No	Submitter	Submission ID	Date (Build)
1	1000GENOMES	ss488679870	May 04, 2012 (137)
2	NHLBI-ESP	ss712338596	Apr 25, 2013 (138)
3	CLINVAR	ss836189133	Oct 23, 2013 (136)
4	EVA-GONL	ss975638414	Apr 09, 2015 (144)
5	F_HASHEMI	ss1026803190	Jun 06, 2014 (141)
6	1000GENOMES	ss1292733474	Aug 28, 2014 (142)
7	EVA_DECODE	ss1585020387	Apr 01, 2015 (144)
8	EVA_UK10K_ALSPAC	ss1601125509	Apr 09, 2015 (144)
9	EVA_UK10K_TWINSUK	ss1644119542	Apr 09, 2015 (144)
10	EVA_EXAC	ss1685735723	Apr 09, 2015 (144)
11	EVA_MGP	ss1710920785	Apr 09, 2015 (144)
12	ILLUMINA	ss1958311328	Feb 17, 2016 (147)
13	USC_VALOUEV	ss2147973132	Oct 11, 2018 (152)
14	GNOMAD	ss2731786776	Oct 11, 2018 (152)
15	GNOMAD	ss2746417678	Oct 11, 2018 (152)
16	GNOMAD	ss2760632227	Oct 11, 2018 (152)
17	SWEGEN	ss2987643051	Oct 11, 2018 (152)
18	ILLUMINA	ss3021129826	Oct 11, 2018 (152)
19	ILLUMINA	ss3651463331	Oct 11, 2018 (152)
20	EVA_DECODE	ss3687688295	Jul 12, 2019 (153)
21	ILLUMINA	ss3725060658	Jul 12, 2019 (153)
22	ACPOP	ss3727447568	Jul 12, 2019 (153)
23	PAGE_CC	ss3770837336	Jul 12, 2019 (153)
24	EVA	ss3823649737	Apr 25, 2020 (154)
25	SGDP_PRJ	ss3849871102	Apr 25, 2020 (154)
26	GNOMAD	ss4002440465	Apr 25, 2021 (155)
27	TOPMED	ss4466441982	Apr 25, 2021 (155)
28	1000G_HIGH_COVERAGE	ss5244093070	Oct 12, 2022 (156)
29	EVA	ss5321704680	Oct 12, 2022 (156)
30	HUGCELL_USP	ss5444753691	Oct 12, 2022 (156)
31	1000G_HIGH_COVERAGE	ss5517322511	Oct 12, 2022 (156)
32	SANFORD_IMAGENETICS	ss5624217086	Oct 12, 2022 (156)
33	SANFORD_IMAGENETICS	ss5626483490	Oct 12, 2022 (156)
34	EVA	ss5832594449	Oct 12, 2022 (156)
35	EVA	ss5847553856	Oct 12, 2022 (156)
36	EVA	ss5910078366	Oct 12, 2022 (156)
37	EVA	ss5938297113	Oct 12, 2022 (156)
38	EVA	ss5979288536	Oct 12, 2022 (156)
39	1000Genomes	NC_000001.10 - 145507765	Oct 11, 2018 (152)
40	1000Genomes_30x	NC_000001.11 - 145927328	Oct 12, 2022 (156)
41	The Avon Longitudinal Study of Parents and Children	NC_000001.10 - 145507765	Oct 11, 2018 (152)
42	ExAC	NC_000001.10 - 145507765	Oct 11, 2018 (152)
43	gnomAD - Genomes	NC_000001.11 - 145927328	Apr 25, 2021 (155)
44	gnomAD - Exomes	NC_000001.10 - 145507765	Jul 12, 2019 (153)
45	GO Exome Sequencing Project	NC_000001.10 - 145507765	Oct 11, 2018 (152)
46	Genome of the Netherlands Release 5	NC_000001.10 - 145507765	Apr 25, 2020 (154)
47	Medical Genome Project healthy controls from Spanish population	NC_000001.10 - 145507765	Apr 25, 2020 (154)
48	Northern Sweden	NC_000001.10 - 145507765	Jul 12, 2019 (153)
49	The PAGE Study	NC_000001.11 - 145927328	Jul 12, 2019 (153)
50	SGDP_PRJ	NC_000001.10 - 145507765	Apr 25, 2020 (154)
51	Siberian	NC_000001.10 - 145507765	Apr 25, 2020 (154)
52	TopMed	NC_000001.11 - 145927328	Apr 25, 2021 (155)
53	UK 10K study - Twins	NC_000001.10 - 145507765	Oct 11, 2018 (152)
54	ALFA	NC_000001.11 - 145927328	Apr 25, 2021 (155)
55	ClinVar	RCV000023419.19	Oct 12, 2022 (156)
56	ClinVar	RCV000172898.14	Oct 12, 2022 (156)
57	ClinVar	RCV001270062.1	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
ss1585020387	NC_000001.9:144219121:G:C	NC_000001.11:145927327:C:G	(self)
3518629, 1922603, 4948426, 805974, 108352, 836911, 37537, 732433, 1888082, 489486, 1922603, ss488679870, ss712338596, ss975638414, ss1292733474, ss1601125509, ss1644119542, ss1685735723, ss1710920785, ss1958311328, ss2147973132, ss2731786776, ss2746417678, ss2760632227, ss2987643051, ss3021129826, ss3651463331, ss3727447568, ss3823649737, ss3849871102, ss5321704680, ss5624217086, ss5626483490, ss5832594449, ss5847553856, ss5938297113, ss5979288536	NC_000001.10:145507764:G:C	NC_000001.11:145927327:C:G	(self)
RCV000023419.19, RCV000172898.14, RCV001270062.1, 4848446, 25420295, 58805, 30048317, 12304919280, ss836189133, ss1026803190, ss3687688295, ss3725060658, ss3770837336, ss4002440465, ss4466441982, ss5244093070, ss5444753691, ss5517322511, ss5910078366	NC_000001.11:145927327:C:G	NC_000001.11:145927327:C:G	(self)

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

3 citations for rs201779890

PMID	Title	Author	Year	Journal
20301781	Thrombocytopenia Absent Radius Syndrome.	Petit F et al.	1993	GeneReviews(®)
22366785	Compound inheritance of a low-frequency regulatory SNP and a rare null mutation in exon-junction complex subunit RBM8A causes TAR syndrome.	Albers CA et al.	2012	Nature genetics
23757202	Free the data: one laboratory's approach to knowledge-based genomic variant classification and preparation for EMR integration of genomic data.	Bean LJ et al.	2013	Human mutation

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
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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.
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dbSNP Short Genetic Variations

Welcome to the Reference SNP (rs) Report

Reference SNP (rs) Report

rs201779890