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dbSNP Short Genetic Variations

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.

rs139428292

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr1:145927447 (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>A / C>G / C>T
Variation Type
SNV Single Nucleotide Variation
Frequency
T=0.017908 (4740/264690, TOPMED)
T=0.018711 (2623/140186, GnomAD)
T=0.02167 (604/27878, ALFA) (+ 15 more)
T=0.02122 (276/13004, GO-ESP)
T=0.0098 (63/6404, 1000G_30x)
T=0.0096 (48/5008, 1000G)
T=0.0358 (138/3854, ALSPAC)
T=0.0286 (106/3708, TWINSUK)
T=0.026 (26/998, GoNL)
T=0.005 (3/600, NorthernSweden)
T=0.028 (15/534, MGP)
T=0.026 (7/274, FINRISK)
T=0.032 (7/216, Qatari)
T=0.03 (1/40, GENOME_DK)
C=0.5 (3/6, SGDP_PRJ)
T=0.5 (3/6, SGDP_PRJ)
C=0.5 (2/4, Siberian)
T=0.5 (2/4, Siberian)
Clinical Significance
Reported in ClinVar
Gene : Consequence
LIX1L-AS1 : Non Coding Transcript Variant
RBM8A : 5 Prime UTR 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 27878 C=0.97833 T=0.02167 0.957314 0.000646 0.04204 1
European Sub 20348 C=0.97562 T=0.02438 0.951936 0.000688 0.047376 0
African Sub 3540 C=0.9918 T=0.0082 0.984181 0.000565 0.015254 4
African Others Sub 122 C=1.000 T=0.000 1.0 0.0 0.0 N/A
African American Sub 3418 C=0.9915 T=0.0085 0.983616 0.000585 0.015799 4
Asian Sub 168 C=1.000 T=0.000 1.0 0.0 0.0 N/A
East Asian Sub 112 C=1.000 T=0.000 1.0 0.0 0.0 N/A
Other Asian Sub 56 C=1.00 T=0.00 1.0 0.0 0.0 N/A
Latin American 1 Sub 146 C=0.973 T=0.027 0.945205 0.0 0.054795 0
Latin American 2 Sub 610 C=0.985 T=0.015 0.970492 0.0 0.029508 0
South Asian Sub 98 C=1.00 T=0.00 1.0 0.0 0.0 N/A
Other Sub 2968 C=0.9778 T=0.0222 0.956199 0.000674 0.043127 0


Help

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
TopMed Global Study-wide 264690 C=0.982092 T=0.017908
gnomAD - Genomes Global Study-wide 140186 C=0.981289 T=0.018711
gnomAD - Genomes European Sub 75934 C=0.97261 T=0.02739
gnomAD - Genomes African Sub 42008 C=0.99402 T=0.00598
gnomAD - Genomes American Sub 13640 C=0.98534 T=0.01466
gnomAD - Genomes Ashkenazi Jewish Sub 3322 C=0.9843 T=0.0157
gnomAD - Genomes East Asian Sub 3130 C=0.9994 T=0.0006
gnomAD - Genomes Other Sub 2152 C=0.9823 T=0.0177
Allele Frequency Aggregator Total Global 27878 C=0.97833 T=0.02167
Allele Frequency Aggregator European Sub 20348 C=0.97562 T=0.02438
Allele Frequency Aggregator African Sub 3540 C=0.9918 T=0.0082
Allele Frequency Aggregator Other Sub 2968 C=0.9778 T=0.0222
Allele Frequency Aggregator Latin American 2 Sub 610 C=0.985 T=0.015
Allele Frequency Aggregator Asian Sub 168 C=1.000 T=0.000
Allele Frequency Aggregator Latin American 1 Sub 146 C=0.973 T=0.027
Allele Frequency Aggregator South Asian Sub 98 C=1.00 T=0.00
GO Exome Sequencing Project Global Study-wide 13004 C=0.97878 T=0.02122
GO Exome Sequencing Project European American Sub 8600 C=0.9713 T=0.0287
GO Exome Sequencing Project African American Sub 4404 C=0.9934 T=0.0066
1000Genomes_30x Global Study-wide 6404 C=0.9902 T=0.0098
1000Genomes_30x African Sub 1786 C=0.9994 T=0.0006
1000Genomes_30x Europe Sub 1266 C=0.9668 T=0.0332
1000Genomes_30x South Asian Sub 1202 C=0.9967 T=0.0033
1000Genomes_30x East Asian Sub 1170 C=1.0000 T=0.0000
1000Genomes_30x American Sub 980 C=0.984 T=0.016
1000Genomes Global Study-wide 5008 C=0.9904 T=0.0096
1000Genomes African Sub 1322 C=0.9992 T=0.0008
1000Genomes East Asian Sub 1008 C=1.0000 T=0.0000
1000Genomes Europe Sub 1006 C=0.9682 T=0.0318
1000Genomes South Asian Sub 978 C=0.996 T=0.004
1000Genomes American Sub 694 C=0.984 T=0.016
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 C=0.9642 T=0.0358
UK 10K study - Twins TWIN COHORT Study-wide 3708 C=0.9714 T=0.0286
Genome of the Netherlands Release 5 Genome of the Netherlands Study-wide 998 C=0.974 T=0.026
Northern Sweden ACPOP Study-wide 600 C=0.995 T=0.005
Medical Genome Project healthy controls from Spanish population Spanish controls Study-wide 534 C=0.972 T=0.028
FINRISK Finnish from FINRISK project Study-wide 274 C=0.974 T=0.026
Qatari Global Study-wide 216 C=0.968 T=0.032
The Danish reference pan genome Danish Study-wide 40 C=0.97 T=0.03
SGDP_PRJ Global Study-wide 6 C=0.5 T=0.5
Siberian Global Study-wide 4 C=0.5 T=0.5
Help

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.145927447C>A
GRCh38.p14 chr 1 NC_000001.11:g.145927447C>G
GRCh38.p14 chr 1 NC_000001.11:g.145927447C>T
GRCh37.p13 chr 1 fix patch HG1287_PATCH NW_003871055.3:g.2742860C>A
GRCh37.p13 chr 1 fix patch HG1287_PATCH NW_003871055.3:g.2742860C>G
GRCh37.p13 chr 1 fix patch HG1287_PATCH NW_003871055.3:g.2742860C>T
RBM8A RefSeqGene (LRG_574) NG_032654.2:g.5090G>T
RBM8A RefSeqGene (LRG_574) NG_032654.2:g.5090G>C
RBM8A RefSeqGene (LRG_574) NG_032654.2:g.5090G>A
LOC126805851 genomic region NG_082175.1:g.1128C>A
LOC126805851 genomic region NG_082175.1:g.1128C>G
LOC126805851 genomic region NG_082175.1:g.1128C>T
GRCh37.p13 chr 1 NC_000001.10:g.145507646G>T
GRCh37.p13 chr 1 NC_000001.10:g.145507646G>C
GRCh37.p13 chr 1 NC_000001.10:g.145507646G>A
Gene: RBM8A, RNA binding motif protein 8A (minus strand)
Molecule type Change Amino acid[Codon] SO Term
RBM8A transcript NM_005105.5:c.-21= N/A 5 Prime UTR 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.500C>A N/A Non Coding Transcript Variant
LIX1L-AS1 transcript NR_147182.1:n.500C>G N/A Non Coding Transcript Variant
LIX1L-AS1 transcript NR_147182.1:n.500C>T N/A Non Coding Transcript Variant
Help

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: T (allele ID: 39421 )
ClinVar Accession Disease Names Clinical Significance
RCV000023418.33 Radial aplasia-thrombocytopenia syndrome Pathogenic-Likely-Pathogenic
RCV000081257.25 not provided Pathogenic,Other
Help

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= A G T
GRCh38.p14 chr 1 NC_000001.11:g.145927447= NC_000001.11:g.145927447C>A NC_000001.11:g.145927447C>G NC_000001.11:g.145927447C>T
GRCh37.p13 chr 1 fix patch HG1287_PATCH NW_003871055.3:g.2742860= NW_003871055.3:g.2742860C>A NW_003871055.3:g.2742860C>G NW_003871055.3:g.2742860C>T
RBM8A RefSeqGene (LRG_574) NG_032654.2:g.5090= NG_032654.2:g.5090G>T NG_032654.2:g.5090G>C NG_032654.2:g.5090G>A
RBM8A transcript NM_005105.5:c.-21= NM_005105.5:c.-21G>T NM_005105.5:c.-21G>C NM_005105.5:c.-21G>A
RBM8A transcript NM_005105.4:c.-21= NM_005105.4:c.-21G>T NM_005105.4:c.-21G>C NM_005105.4:c.-21G>A
LOC126805851 genomic region NG_082175.1:g.1128= NG_082175.1:g.1128C>A NG_082175.1:g.1128C>G NG_082175.1:g.1128C>T
GRCh37.p13 chr 1 NC_000001.10:g.145507646= NC_000001.10:g.145507646G>T NC_000001.10:g.145507646G>C NC_000001.10:g.145507646G>A
LIX1L-AS1 transcript NR_147182.1:n.500= NR_147182.1:n.500C>A NR_147182.1:n.500C>G NR_147182.1:n.500C>T
Help

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#.

55 SubSNP, 20 Frequency, 2 ClinVar submissions
No Submitter Submission ID Date (Build)
1 BL ss253467047 May 09, 2011 (134)
2 1000GENOMES ss328916448 May 09, 2011 (134)
3 1000GENOMES ss489760991 May 04, 2012 (137)
4 CLINSEQ_SNP ss491602072 May 04, 2012 (137)
5 SSMP ss648379162 Apr 25, 2013 (138)
6 NHLBI-ESP ss712338592 Apr 25, 2013 (138)
7 EVA-GONL ss975638413 Apr 09, 2015 (144)
8 F_HASHEMI ss1026803189 Jun 06, 2014 (141)
9 1000GENOMES ss1292733471 Aug 28, 2014 (142)
10 EVA_GENOME_DK ss1574366507 Apr 09, 2015 (144)
11 EVA_FINRISK ss1584010574 Apr 09, 2015 (144)
12 EVA_DECODE ss1585020384 Apr 01, 2015 (144)
13 EVA_UK10K_ALSPAC ss1601125507 Apr 09, 2015 (144)
14 EVA_UK10K_TWINSUK ss1644119540 Apr 09, 2015 (144)
15 EVA_EXAC ss1685735706 Apr 09, 2015 (144)
16 EVA_EXAC ss1685735707 Apr 09, 2015 (144)
17 EVA_MGP ss1710920784 Apr 09, 2015 (144)
18 WEILL_CORNELL_DGM ss1918860799 Feb 17, 2016 (147)
19 ILLUMINA ss1958311327 Feb 17, 2016 (147)
20 JJLAB ss2019949767 Sep 28, 2016 (149)
21 USC_VALOUEV ss2147973131 Oct 11, 2018 (152)
22 GNOMAD ss2731786743 Oct 11, 2018 (152)
23 GNOMAD ss2746417670 Oct 11, 2018 (152)
24 GNOMAD ss2760632219 Oct 11, 2018 (152)
25 SWEGEN ss2987643050 Oct 11, 2018 (152)
26 ILLUMINA ss3021129825 Oct 11, 2018 (152)
27 CSHL ss3343684769 Oct 11, 2018 (152)
28 OMUKHERJEE_ADBS ss3646241194 Oct 11, 2018 (152)
29 ILLUMINA ss3651463330 Oct 11, 2018 (152)
30 EVA_DECODE ss3687688298 Jul 12, 2019 (153)
31 ACPOP ss3727447567 Jul 12, 2019 (153)
32 EVA ss3823649732 Apr 25, 2020 (154)
33 EVA ss3825573580 Apr 25, 2020 (154)
34 EVA ss3836593846 Apr 25, 2020 (154)
35 EVA ss3842005148 Apr 25, 2020 (154)
36 SGDP_PRJ ss3849871100 Apr 25, 2020 (154)
37 FSA-LAB ss3983943551 Apr 25, 2021 (155)
38 EVA ss3986134574 Apr 25, 2021 (155)
39 GNOMAD ss4002440483 Apr 25, 2021 (155)
40 TOPMED ss4466442016 Apr 25, 2021 (155)
41 1000G_HIGH_COVERAGE ss5244093073 Oct 12, 2022 (156)
42 EVA ss5321704675 Oct 12, 2022 (156)
43 HUGCELL_USP ss5444753696 Oct 12, 2022 (156)
44 HUGCELL_USP ss5444753697 Oct 12, 2022 (156)
45 1000G_HIGH_COVERAGE ss5517322515 Oct 12, 2022 (156)
46 EVA ss5623996639 Oct 12, 2022 (156)
47 SANFORD_IMAGENETICS ss5624217085 Oct 12, 2022 (156)
48 SANFORD_IMAGENETICS ss5626483489 Oct 12, 2022 (156)
49 EVA ss5832594448 Oct 12, 2022 (156)
50 EVA ss5847166254 Oct 12, 2022 (156)
51 EVA ss5847553855 Oct 12, 2022 (156)
52 EVA ss5848270002 Oct 12, 2022 (156)
53 EVA ss5910078370 Oct 12, 2022 (156)
54 EVA ss5938297111 Oct 12, 2022 (156)
55 EVA ss5979288535 Oct 12, 2022 (156)
56 1000Genomes NC_000001.10 - 145507646 Oct 11, 2018 (152)
57 1000Genomes_30x NC_000001.11 - 145927447 Oct 12, 2022 (156)
58 The Avon Longitudinal Study of Parents and Children NC_000001.10 - 145507646 Oct 11, 2018 (152)
59 ExAC

Submission ignored due to conflicting rows:
Row 4948407 (NC_000001.10:145507645:G:G 80742/82700, NC_000001.10:145507645:G:A 1958/82700)
Row 4948408 (NC_000001.10:145507645:G:G 82699/82700, NC_000001.10:145507645:G:T 1/82700)

- Oct 11, 2018 (152)
60 ExAC

Submission ignored due to conflicting rows:
Row 4948407 (NC_000001.10:145507645:G:G 80742/82700, NC_000001.10:145507645:G:A 1958/82700)
Row 4948408 (NC_000001.10:145507645:G:G 82699/82700, NC_000001.10:145507645:G:T 1/82700)

- Oct 11, 2018 (152)
61 FINRISK NC_000001.10 - 145507646 Apr 25, 2020 (154)
62 The Danish reference pan genome NC_000001.10 - 145507646 Apr 25, 2020 (154)
63 gnomAD - Genomes NC_000001.11 - 145927447 Apr 25, 2021 (155)
64 gnomAD - Exomes

Submission ignored due to conflicting rows:
Row 805942 (NC_000001.10:145507645:G:G 233536/237842, NC_000001.10:145507645:G:A 4306/237842)
Row 805943 (NC_000001.10:145507645:G:G 237841/237842, NC_000001.10:145507645:G:T 1/237842)

- Jul 12, 2019 (153)
65 gnomAD - Exomes

Submission ignored due to conflicting rows:
Row 805942 (NC_000001.10:145507645:G:G 233536/237842, NC_000001.10:145507645:G:A 4306/237842)
Row 805943 (NC_000001.10:145507645:G:G 237841/237842, NC_000001.10:145507645:G:T 1/237842)

- Jul 12, 2019 (153)
66 GO Exome Sequencing Project NC_000001.10 - 145507646 Oct 11, 2018 (152)
67 Genome of the Netherlands Release 5 NC_000001.10 - 145507646 Apr 25, 2020 (154)
68 Medical Genome Project healthy controls from Spanish population NC_000001.10 - 145507646 Apr 25, 2020 (154)
69 Northern Sweden NC_000001.10 - 145507646 Jul 12, 2019 (153)
70 Qatari NC_000001.10 - 145507646 Apr 25, 2020 (154)
71 SGDP_PRJ NC_000001.10 - 145507646 Apr 25, 2020 (154)
72 Siberian NC_000001.10 - 145507646 Apr 25, 2020 (154)
73 TopMed NC_000001.11 - 145927447 Apr 25, 2021 (155)
74 UK 10K study - Twins NC_000001.10 - 145507646 Oct 11, 2018 (152)
75 ALFA NC_000001.11 - 145927447 Apr 25, 2021 (155)
76 ClinVar RCV000023418.33 Oct 12, 2022 (156)
77 ClinVar RCV000081257.25 Oct 12, 2022 (156)
Help

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
ss1685735707, ss2731786743 NC_000001.10:145507645:G:T NC_000001.11:145927446:C:A (self)
ss5444753697 NC_000001.11:145927446:C:G NC_000001.11:145927446:C:G
ss253467047, ss491602072, ss1585020384 NC_000001.9:144219002:G:A NC_000001.11:145927446:C:T (self)
3518626, 1922601, 7035, 1692163, 108347, 836910, 37536, 732432, 902729, 1888080, 489485, 1922601, ss328916448, ss489760991, ss648379162, ss712338592, ss975638413, ss1292733471, ss1574366507, ss1584010574, ss1601125507, ss1644119540, ss1685735706, ss1710920784, ss1918860799, ss1958311327, ss2019949767, ss2147973131, ss2731786743, ss2746417670, ss2760632219, ss2987643050, ss3021129825, ss3343684769, ss3646241194, ss3651463330, ss3727447567, ss3823649732, ss3825573580, ss3836593846, ss3849871100, ss3983943551, ss3986134574, ss5321704675, ss5623996639, ss5624217085, ss5626483489, ss5832594448, ss5847166254, ss5847553855, ss5848270002, ss5938297111, ss5979288535 NC_000001.10:145507645:G:A NC_000001.11:145927446:C:T (self)
RCV000023418.33, RCV000081257.25, 4848450, 25420313, 30048351, 8555259718, ss1026803189, ss3687688298, ss3842005148, ss4002440483, ss4466442016, ss5244093073, ss5444753696, ss5517322515, ss5910078370 NC_000001.11:145927446:C:T NC_000001.11:145927446:C:T (self)
Help

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

3 citations for rs139428292
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
Help

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.

Software version is: 2.0.1.post825+45319f0