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dbSNP Short Genetic Variations

Examples: rs268, BRCA1 and more Advanced search

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.

rs139464798

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr18:13752333 (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>T
Variation Type
SNV Single Nucleotide Variation
Frequency
T=0.000570 (151/264690, TOPMED)
T=0.000147 (37/251034, GnomAD_exome)
T=0.000024 (4/163764, ALFA) (+ 6 more)
T=0.000657 (92/140116, GnomAD)
T=0.000183 (22/120504, ExAC)
T=0.00103 (81/78696, PAGE_STUDY)
T=0.00046 (6/13006, GO-ESP)
T=0.0005 (3/6404, 1000G_30x)
T=0.0006 (3/5008, 1000G)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
RNMT : Missense 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: 20230706150541
Population Group Sample Size Ref Allele Alt Allele
Total Global 180130 C=0.999933 T=0.000067
European Sub 156970 C=1.000000 T=0.000000
African Sub 9118 C=0.9988 T=0.0012
African Others Sub 352 C=0.994 T=0.006
African American Sub 8766 C=0.9990 T=0.0010
Asian Sub 3338 C=1.0000 T=0.0000
East Asian Sub 2686 C=1.0000 T=0.0000
Other Asian Sub 652 C=1.000 T=0.000
Latin American 1 Sub 442 C=1.000 T=0.000
Latin American 2 Sub 950 C=1.000 T=0.000
South Asian Sub 280 C=1.000 T=0.000
Other Sub 9032 C=0.9999 T=0.0001


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=0.999430 T=0.000570
gnomAD - Exomes Global Study-wide 251034 C=0.999853 T=0.000147
gnomAD - Exomes European Sub 135164 C=1.000000 T=0.000000
gnomAD - Exomes Asian Sub 48978 C=1.00000 T=0.00000
gnomAD - Exomes American Sub 34462 C=0.99991 T=0.00009
gnomAD - Exomes African Sub 16244 C=0.99791 T=0.00209
gnomAD - Exomes Ashkenazi Jewish Sub 10072 C=1.00000 T=0.00000
gnomAD - Exomes Other Sub 6114 C=1.0000 T=0.0000
Allele Frequency Aggregator Total Global 163764 C=0.999976 T=0.000024
Allele Frequency Aggregator European Sub 146852 C=1.000000 T=0.000000
Allele Frequency Aggregator Other Sub 7610 C=1.0000 T=0.0000
Allele Frequency Aggregator African Sub 4292 C=0.9991 T=0.0009
Allele Frequency Aggregator Asian Sub 3338 C=1.0000 T=0.0000
Allele Frequency Aggregator Latin American 2 Sub 950 C=1.000 T=0.000
Allele Frequency Aggregator Latin American 1 Sub 442 C=1.000 T=0.000
Allele Frequency Aggregator South Asian Sub 280 C=1.000 T=0.000
gnomAD - Genomes Global Study-wide 140116 C=0.999343 T=0.000657
gnomAD - Genomes European Sub 75906 C=1.00000 T=0.00000
gnomAD - Genomes African Sub 41968 C=0.99781 T=0.00219
gnomAD - Genomes American Sub 13646 C=1.00000 T=0.00000
gnomAD - Genomes Ashkenazi Jewish Sub 3318 C=1.0000 T=0.0000
gnomAD - Genomes East Asian Sub 3132 C=1.0000 T=0.0000
gnomAD - Genomes Other Sub 2146 C=1.0000 T=0.0000
ExAC Global Study-wide 120504 C=0.999817 T=0.000183
ExAC Europe Sub 72734 C=1.00000 T=0.00000
ExAC Asian Sub 25024 C=1.00000 T=0.00000
ExAC American Sub 11534 C=0.99991 T=0.00009
ExAC African Sub 10314 C=0.99796 T=0.00204
ExAC Other Sub 898 C=1.000 T=0.000
The PAGE Study Global Study-wide 78696 C=0.99897 T=0.00103
The PAGE Study AfricanAmerican Sub 32516 C=0.99785 T=0.00215
The PAGE Study Mexican Sub 10808 C=0.99963 T=0.00037
The PAGE Study Asian Sub 8316 C=1.0000 T=0.0000
The PAGE Study PuertoRican Sub 7916 C=0.9994 T=0.0006
The PAGE Study NativeHawaiian Sub 4534 C=1.0000 T=0.0000
The PAGE Study Cuban Sub 4230 C=1.0000 T=0.0000
The PAGE Study Dominican Sub 3828 C=0.9997 T=0.0003
The PAGE Study CentralAmerican Sub 2450 C=1.0000 T=0.0000
The PAGE Study SouthAmerican Sub 1982 C=0.9995 T=0.0005
The PAGE Study NativeAmerican Sub 1260 C=1.0000 T=0.0000
The PAGE Study SouthAsian Sub 856 C=1.000 T=0.000
GO Exome Sequencing Project Global Study-wide 13006 C=0.99954 T=0.00046
GO Exome Sequencing Project European American Sub 8600 C=1.0000 T=0.0000
GO Exome Sequencing Project African American Sub 4406 C=0.9986 T=0.0014
1000Genomes_30x Global Study-wide 6404 C=0.9995 T=0.0005
1000Genomes_30x African Sub 1786 C=0.9983 T=0.0017
1000Genomes_30x Europe Sub 1266 C=1.0000 T=0.0000
1000Genomes_30x South Asian Sub 1202 C=1.0000 T=0.0000
1000Genomes_30x East Asian Sub 1170 C=1.0000 T=0.0000
1000Genomes_30x American Sub 980 C=1.000 T=0.000
1000Genomes Global Study-wide 5008 C=0.9994 T=0.0006
1000Genomes African Sub 1322 C=0.9977 T=0.0023
1000Genomes East Asian Sub 1008 C=1.0000 T=0.0000
1000Genomes Europe Sub 1006 C=1.0000 T=0.0000
1000Genomes South Asian Sub 978 C=1.000 T=0.000
1000Genomes American Sub 694 C=1.000 T=0.000
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 18 NC_000018.10:g.13752333C>T
GRCh37.p13 chr 18 NC_000018.9:g.13752332C>T
Gene: RNMT, RNA guanine-7 methyltransferase (plus strand)
Molecule type Change Amino acid[Codon] SO Term
RNMT transcript variant 1 NM_001308263.2:c.1265C>T P [CCT] > L [CTT] Coding Sequence Variant
mRNA cap guanine-N7 methyltransferase isoform 1 NP_001295192.1:p.Pro422Leu P (Pro) > L (Leu) Missense Variant
RNMT transcript variant 2 NM_003799.3:c.1265C>T P [CCT] > L [CTT] Coding Sequence Variant
mRNA cap guanine-N7 methyltransferase isoform 2 NP_003790.1:p.Pro422Leu P (Pro) > L (Leu) Missense Variant
RNMT transcript variant 5 NM_001378135.1:c.1265C>T P [CCT] > L [CTT] Coding Sequence Variant
mRNA cap guanine-N7 methyltransferase isoform 2 NP_001365064.1:p.Pro422Leu P (Pro) > L (Leu) Missense Variant
RNMT transcript variant 4 NM_001378134.1:c.1265C>T P [CCT] > L [CTT] Coding Sequence Variant
mRNA cap guanine-N7 methyltransferase isoform 1 NP_001365063.1:p.Pro422Leu P (Pro) > L (Leu) Missense Variant
RNMT transcript variant 3 NM_001378132.1:c.731C>T P [CCT] > L [CTT] Coding Sequence Variant
mRNA cap guanine-N7 methyltransferase isoform 3 NP_001365061.1:p.Pro244Leu P (Pro) > L (Leu) Missense Variant
RNMT transcript variant 6 NR_165427.1:n.1493C>T N/A Non Coding Transcript Variant
RNMT transcript variant X1 XM_011525749.3:c.1265C>T P [CCT] > L [CTT] Coding Sequence Variant
mRNA cap guanine-N7 methyltransferase isoform X1 XP_011524051.1:p.Pro422Leu P (Pro) > L (Leu) Missense Variant
RNMT transcript variant X2 XM_011525750.3:c.1265C>T P [CCT] > L [CTT] Coding Sequence Variant
mRNA cap guanine-N7 methyltransferase isoform X1 XP_011524052.1:p.Pro422Leu P (Pro) > L (Leu) Missense Variant
RNMT transcript variant X3 XM_011525751.2:c.1265C>T P [CCT] > L [CTT] Coding Sequence Variant
mRNA cap guanine-N7 methyltransferase isoform X1 XP_011524053.1:p.Pro422Leu P (Pro) > L (Leu) Missense Variant
RNMT transcript variant X4 XM_047437907.1:c.1265C>T P [CCT] > L [CTT] Coding Sequence Variant
mRNA cap guanine-N7 methyltransferase isoform X2 XP_047293863.1:p.Pro422Leu P (Pro) > L (Leu) Missense Variant
RNMT transcript variant X5 XM_047437908.1:c.1265C>T P [CCT] > L [CTT] Coding Sequence Variant
mRNA cap guanine-N7 methyltransferase isoform X3 XP_047293864.1:p.Pro422Leu P (Pro) > L (Leu) Missense Variant
RNMT transcript variant X6 XM_011525753.3:c.731C>T P [CCT] > L [CTT] Coding Sequence Variant
mRNA cap guanine-N7 methyltransferase isoform X4 XP_011524055.1:p.Pro244Leu P (Pro) > L (Leu) Missense 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.

Not Reported in ClinVar
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= T
GRCh38.p14 chr 18 NC_000018.10:g.13752333= NC_000018.10:g.13752333C>T
GRCh37.p13 chr 18 NC_000018.9:g.13752332= NC_000018.9:g.13752332C>T
RNMT transcript variant X1 XM_011525749.3:c.1265= XM_011525749.3:c.1265C>T
RNMT transcript variant X1 XM_011525749.2:c.1265= XM_011525749.2:c.1265C>T
RNMT transcript variant X1 XM_011525749.1:c.1265= XM_011525749.1:c.1265C>T
RNMT transcript variant 2 NM_003799.3:c.1265= NM_003799.3:c.1265C>T
RNMT transcript variant 2 NM_003799.2:c.1265= NM_003799.2:c.1265C>T
RNMT transcript NM_003799.1:c.1265= NM_003799.1:c.1265C>T
RNMT transcript variant X2 XM_011525750.3:c.1265= XM_011525750.3:c.1265C>T
RNMT transcript variant X2 XM_011525750.2:c.1265= XM_011525750.2:c.1265C>T
RNMT transcript variant X2 XM_011525750.1:c.1265= XM_011525750.1:c.1265C>T
RNMT transcript variant X6 XM_011525753.3:c.731= XM_011525753.3:c.731C>T
RNMT transcript variant X8 XM_011525753.2:c.731= XM_011525753.2:c.731C>T
RNMT transcript variant X8 XM_011525753.1:c.731= XM_011525753.1:c.731C>T
RNMT transcript variant X3 XM_011525751.2:c.1265= XM_011525751.2:c.1265C>T
RNMT transcript variant X3 XM_011525751.1:c.1265= XM_011525751.1:c.1265C>T
RNMT transcript variant 1 NM_001308263.2:c.1265= NM_001308263.2:c.1265C>T
RNMT transcript variant 1 NM_001308263.1:c.1265= NM_001308263.1:c.1265C>T
RNMT transcript variant X5 XM_047437908.1:c.1265= XM_047437908.1:c.1265C>T
RNMT transcript variant 5 NM_001378135.1:c.1265= NM_001378135.1:c.1265C>T
RNMT transcript variant 3 NM_001378132.1:c.731= NM_001378132.1:c.731C>T
RNMT transcript variant 6 NR_165427.1:n.1493= NR_165427.1:n.1493C>T
RNMT transcript variant X4 XM_047437907.1:c.1265= XM_047437907.1:c.1265C>T
RNMT transcript variant 4 NM_001378134.1:c.1265= NM_001378134.1:c.1265C>T
mRNA cap guanine-N7 methyltransferase isoform X1 XP_011524051.1:p.Pro422= XP_011524051.1:p.Pro422Leu
mRNA cap guanine-N7 methyltransferase isoform 2 NP_003790.1:p.Pro422= NP_003790.1:p.Pro422Leu
mRNA cap guanine-N7 methyltransferase isoform X1 XP_011524052.1:p.Pro422= XP_011524052.1:p.Pro422Leu
mRNA cap guanine-N7 methyltransferase isoform X4 XP_011524055.1:p.Pro244= XP_011524055.1:p.Pro244Leu
mRNA cap guanine-N7 methyltransferase isoform X1 XP_011524053.1:p.Pro422= XP_011524053.1:p.Pro422Leu
mRNA cap guanine-N7 methyltransferase isoform 1 NP_001295192.1:p.Pro422= NP_001295192.1:p.Pro422Leu
mRNA cap guanine-N7 methyltransferase isoform X3 XP_047293864.1:p.Pro422= XP_047293864.1:p.Pro422Leu
mRNA cap guanine-N7 methyltransferase isoform 2 NP_001365064.1:p.Pro422= NP_001365064.1:p.Pro422Leu
mRNA cap guanine-N7 methyltransferase isoform 3 NP_001365061.1:p.Pro244= NP_001365061.1:p.Pro244Leu
mRNA cap guanine-N7 methyltransferase isoform X2 XP_047293863.1:p.Pro422= XP_047293863.1:p.Pro422Leu
mRNA cap guanine-N7 methyltransferase isoform 1 NP_001365063.1:p.Pro422= NP_001365063.1:p.Pro422Leu
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#.

37 SubSNP, 9 Frequency submissions
No Submitter Submission ID Date (Build)
1 NHLBI-ESP ss342471823 May 09, 2011 (134)
2 EXOME_CHIP ss491531605 May 04, 2012 (137)
3 ILLUMINA ss780735209 Sep 08, 2015 (146)
4 ILLUMINA ss783411987 Sep 08, 2015 (146)
5 1000GENOMES ss1360227904 Aug 21, 2014 (142)
6 EVA_EXAC ss1693093419 Apr 01, 2015 (144)
7 ILLUMINA ss1752247849 Sep 08, 2015 (146)
8 ILLUMINA ss1917925880 Feb 12, 2016 (147)
9 ILLUMINA ss1946489760 Feb 12, 2016 (147)
10 ILLUMINA ss1959790347 Feb 12, 2016 (147)
11 HUMAN_LONGEVITY ss2220007519 Dec 20, 2016 (150)
12 GNOMAD ss2743208067 Nov 08, 2017 (151)
13 GNOMAD ss2749930734 Nov 08, 2017 (151)
14 GNOMAD ss2954376795 Nov 08, 2017 (151)
15 AFFY ss2985113465 Nov 08, 2017 (151)
16 AFFY ss2985750284 Nov 08, 2017 (151)
17 ILLUMINA ss3021826875 Nov 08, 2017 (151)
18 ILLUMINA ss3627767268 Oct 12, 2018 (152)
19 ILLUMINA ss3634697654 Oct 12, 2018 (152)
20 ILLUMINA ss3640404963 Oct 12, 2018 (152)
21 ILLUMINA ss3644701697 Oct 12, 2018 (152)
22 ILLUMINA ss3652246723 Oct 12, 2018 (152)
23 ILLUMINA ss3653885322 Oct 12, 2018 (152)
24 ILLUMINA ss3725661950 Jul 13, 2019 (153)
25 ILLUMINA ss3744452508 Jul 13, 2019 (153)
26 ILLUMINA ss3744997821 Jul 13, 2019 (153)
27 PAGE_CC ss3771960977 Jul 13, 2019 (153)
28 ILLUMINA ss3772495388 Jul 13, 2019 (153)
29 EVA ss3825180999 Apr 27, 2020 (154)
30 TOPMED ss5049518302 Apr 27, 2021 (155)
31 1000G_HIGH_COVERAGE ss5304558831 Oct 16, 2022 (156)
32 EVA ss5430138051 Oct 16, 2022 (156)
33 HUGCELL_USP ss5497450936 Oct 16, 2022 (156)
34 1000G_HIGH_COVERAGE ss5608933001 Oct 16, 2022 (156)
35 EVA ss5847815678 Oct 16, 2022 (156)
36 EVA ss5873295155 Oct 16, 2022 (156)
37 EVA ss5952301936 Oct 16, 2022 (156)
38 1000Genomes NC_000018.9 - 13752332 Oct 12, 2018 (152)
39 1000Genomes_30x NC_000018.10 - 13752333 Oct 16, 2022 (156)
40 ExAC NC_000018.9 - 13752332 Oct 12, 2018 (152)
41 gnomAD - Genomes NC_000018.10 - 13752333 Apr 27, 2021 (155)
42 gnomAD - Exomes NC_000018.9 - 13752332 Jul 13, 2019 (153)
43 GO Exome Sequencing Project NC_000018.9 - 13752332 Oct 12, 2018 (152)
44 The PAGE Study NC_000018.10 - 13752333 Jul 13, 2019 (153)
45 TopMed NC_000018.10 - 13752333 Apr 27, 2021 (155)
46 ALFA NC_000018.10 - 13752333 Apr 27, 2021 (155)
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
73529271, 3560511, 12518137, 1638029, ss342471823, ss491531605, ss780735209, ss783411987, ss1360227904, ss1693093419, ss1752247849, ss1917925880, ss1946489760, ss1959790347, ss2743208067, ss2749930734, ss2954376795, ss2985113465, ss2985750284, ss3021826875, ss3627767268, ss3634697654, ss3640404963, ss3644701697, ss3652246723, ss3653885322, ss3744452508, ss3744997821, ss3772495388, ss3825180999, ss5430138051, ss5847815678, ss5952301936 NC_000018.9:13752331:C:T NC_000018.10:13752332:C:T (self)
96458936, 518676328, 1182446, 265063965, 4235204072, ss2220007519, ss3725661950, ss3771960977, ss5049518302, ss5304558831, ss5497450936, ss5608933001, ss5873295155 NC_000018.10:13752332:C:T NC_000018.10:13752332: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.

No publications for rs139464798

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.post761+d5e8e07