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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.

rs146593760

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr12:56093776 (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
A>T
Variation Type
SNV Single Nucleotide Variation
Frequency
T=0.000586 (155/264690, TOPMED)
T=0.000796 (200/251354, GnomAD_exome)
T=0.000243 (34/140138, GnomAD) (+ 10 more)
T=0.000799 (97/121370, ExAC)
T=0.00037 (33/88746, ALFA)
T=0.00090 (71/78700, PAGE_STUDY)
T=0.00520 (147/28258, 14KJPN)
T=0.00549 (92/16760, 8.3KJPN)
T=0.0012 (8/6404, 1000G_30x)
T=0.0014 (7/5008, 1000G)
T=0.0130 (38/2922, KOREAN)
T=0.0104 (19/1832, Korea1K)
T=0.011 (9/792, PRJEB37584)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
ERBB3 : 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 88746 A=0.99963 T=0.00037
European Sub 75504 A=0.99999 T=0.00001
African Sub 4334 A=1.0000 T=0.0000
African Others Sub 174 A=1.000 T=0.000
African American Sub 4160 A=1.0000 T=0.0000
Asian Sub 3328 A=0.9910 T=0.0090
East Asian Sub 2672 A=0.9895 T=0.0105
Other Asian Sub 656 A=0.997 T=0.003
Latin American 1 Sub 436 A=1.000 T=0.000
Latin American 2 Sub 928 A=1.000 T=0.000
South Asian Sub 274 A=0.993 T=0.007
Other Sub 3942 A=1.0000 T=0.0000


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 A=0.999414 T=0.000586
gnomAD - Exomes Global Study-wide 251354 A=0.999204 T=0.000796
gnomAD - Exomes European Sub 135288 A=0.999978 T=0.000022
gnomAD - Exomes Asian Sub 49010 A=0.99598 T=0.00402
gnomAD - Exomes American Sub 34588 A=1.00000 T=0.00000
gnomAD - Exomes African Sub 16254 A=1.00000 T=0.00000
gnomAD - Exomes Ashkenazi Jewish Sub 10078 A=1.00000 T=0.00000
gnomAD - Exomes Other Sub 6136 A=1.0000 T=0.0000
gnomAD - Genomes Global Study-wide 140138 A=0.999757 T=0.000243
gnomAD - Genomes European Sub 75882 A=0.99999 T=0.00001
gnomAD - Genomes African Sub 42002 A=1.00000 T=0.00000
gnomAD - Genomes American Sub 13652 A=1.00000 T=0.00000
gnomAD - Genomes Ashkenazi Jewish Sub 3318 A=1.0000 T=0.0000
gnomAD - Genomes East Asian Sub 3130 A=0.9904 T=0.0096
gnomAD - Genomes Other Sub 2154 A=0.9986 T=0.0014
ExAC Global Study-wide 121370 A=0.999201 T=0.000799
ExAC Europe Sub 73330 A=0.99999 T=0.00001
ExAC Asian Sub 25160 A=0.99622 T=0.00378
ExAC American Sub 11576 A=1.00000 T=0.00000
ExAC African Sub 10396 A=1.00000 T=0.00000
ExAC Other Sub 908 A=0.999 T=0.001
Allele Frequency Aggregator Total Global 88746 A=0.99963 T=0.00037
Allele Frequency Aggregator European Sub 75504 A=0.99999 T=0.00001
Allele Frequency Aggregator African Sub 4334 A=1.0000 T=0.0000
Allele Frequency Aggregator Other Sub 3942 A=1.0000 T=0.0000
Allele Frequency Aggregator Asian Sub 3328 A=0.9910 T=0.0090
Allele Frequency Aggregator Latin American 2 Sub 928 A=1.000 T=0.000
Allele Frequency Aggregator Latin American 1 Sub 436 A=1.000 T=0.000
Allele Frequency Aggregator South Asian Sub 274 A=0.993 T=0.007
The PAGE Study Global Study-wide 78700 A=0.99910 T=0.00090
The PAGE Study AfricanAmerican Sub 32516 A=1.00000 T=0.00000
The PAGE Study Mexican Sub 10810 A=1.00000 T=0.00000
The PAGE Study Asian Sub 8318 A=0.9928 T=0.0072
The PAGE Study PuertoRican Sub 7916 A=1.0000 T=0.0000
The PAGE Study NativeHawaiian Sub 4534 A=0.9982 T=0.0018
The PAGE Study Cuban Sub 4230 A=0.9998 T=0.0002
The PAGE Study Dominican Sub 3828 A=1.0000 T=0.0000
The PAGE Study CentralAmerican Sub 2450 A=1.0000 T=0.0000
The PAGE Study SouthAmerican Sub 1982 A=0.9995 T=0.0005
The PAGE Study NativeAmerican Sub 1260 A=1.0000 T=0.0000
The PAGE Study SouthAsian Sub 856 A=0.999 T=0.001
14KJPN JAPANESE Study-wide 28258 A=0.99480 T=0.00520
8.3KJPN JAPANESE Study-wide 16760 A=0.99451 T=0.00549
1000Genomes_30x Global Study-wide 6404 A=0.9988 T=0.0012
1000Genomes_30x African Sub 1786 A=1.0000 T=0.0000
1000Genomes_30x Europe Sub 1266 A=1.0000 T=0.0000
1000Genomes_30x South Asian Sub 1202 A=1.0000 T=0.0000
1000Genomes_30x East Asian Sub 1170 A=0.9932 T=0.0068
1000Genomes_30x American Sub 980 A=1.000 T=0.000
1000Genomes Global Study-wide 5008 A=0.9986 T=0.0014
1000Genomes African Sub 1322 A=1.0000 T=0.0000
1000Genomes East Asian Sub 1008 A=0.9931 T=0.0069
1000Genomes Europe Sub 1006 A=1.0000 T=0.0000
1000Genomes South Asian Sub 978 A=1.000 T=0.000
1000Genomes American Sub 694 A=1.000 T=0.000
KOREAN population from KRGDB KOREAN Study-wide 2922 A=0.9870 T=0.0130
Korean Genome Project KOREAN Study-wide 1832 A=0.9896 T=0.0104
CNV burdens in cranial meningiomas Global Study-wide 792 A=0.989 T=0.011
CNV burdens in cranial meningiomas CRM Sub 792 A=0.989 T=0.011
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 12 NC_000012.12:g.56093776A>T
GRCh37.p13 chr 12 NC_000012.11:g.56487560A>T
ERBB3 RefSeqGene (LRG_996) NG_011529.1:g.18669A>T
Gene: ERBB3, erb-b2 receptor tyrosine kinase 3 (plus strand)
Molecule type Change Amino acid[Codon] SO Term
ERBB3 transcript variant s NM_001005915.1:c. N/A Genic Downstream Transcript Variant
ERBB3 transcript variant 1 NM_001982.4:c.1493A>T K [AAA] > I [ATA] Coding Sequence Variant
receptor tyrosine-protein kinase erbB-3 isoform 1 precursor NP_001973.2:p.Lys498Ile K (Lys) > I (Ile) Missense Variant
ERBB3 transcript variant X1 XM_047428500.1:c.1316A>T K [AAA] > I [ATA] Coding Sequence Variant
receptor tyrosine-protein kinase erbB-3 isoform X1 XP_047284456.1:p.Lys439Ile K (Lys) > I (Ile) Missense Variant
ERBB3 transcript variant X2 XM_047428501.1:c.1316A>T K [AAA] > I [ATA] Coding Sequence Variant
receptor tyrosine-protein kinase erbB-3 isoform X1 XP_047284457.1:p.Lys439Ile K (Lys) > I (Ile) 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 A= T
GRCh38.p14 chr 12 NC_000012.12:g.56093776= NC_000012.12:g.56093776A>T
GRCh37.p13 chr 12 NC_000012.11:g.56487560= NC_000012.11:g.56487560A>T
ERBB3 RefSeqGene (LRG_996) NG_011529.1:g.18669= NG_011529.1:g.18669A>T
ERBB3 transcript variant 1 NM_001982.4:c.1493= NM_001982.4:c.1493A>T
ERBB3 transcript variant 1 NM_001982.3:c.1493= NM_001982.3:c.1493A>T
ERBB3 transcript variant X2 XM_047428501.1:c.1316= XM_047428501.1:c.1316A>T
ERBB3 transcript variant X1 XM_047428500.1:c.1316= XM_047428500.1:c.1316A>T
receptor tyrosine-protein kinase erbB-3 isoform 1 precursor NP_001973.2:p.Lys498= NP_001973.2:p.Lys498Ile
receptor tyrosine-protein kinase erbB-3 isoform X1 XP_047284457.1:p.Lys439= XP_047284457.1:p.Lys439Ile
receptor tyrosine-protein kinase erbB-3 isoform X1 XP_047284456.1:p.Lys439= XP_047284456.1:p.Lys439Ile
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#.

53 SubSNP, 13 Frequency submissions
No Submitter Submission ID Date (Build)
1 GMI ss281408661 May 04, 2012 (137)
2 1000GENOMES ss337368359 May 09, 2011 (134)
3 1000GENOMES ss491044665 May 04, 2012 (137)
4 EXOME_CHIP ss491469462 May 04, 2012 (137)
5 ILLUMINA ss534382934 Sep 08, 2015 (146)
6 ILLUMINA ss780772829 Aug 21, 2014 (142)
7 ILLUMINA ss783452567 Aug 21, 2014 (142)
8 1000GENOMES ss1345141783 Aug 21, 2014 (142)
9 EVA_EXAC ss1690956035 Apr 01, 2015 (144)
10 ILLUMINA ss1752073790 Sep 08, 2015 (146)
11 ILLUMINA ss1917875021 Feb 12, 2016 (147)
12 ILLUMINA ss1946340480 Feb 12, 2016 (147)
13 ILLUMINA ss1959438391 Feb 12, 2016 (147)
14 AMU ss1966651761 Feb 12, 2016 (147)
15 HUMAN_LONGEVITY ss2190042330 Dec 20, 2016 (150)
16 GNOMAD ss2739890947 Nov 08, 2017 (151)
17 GNOMAD ss2748889756 Nov 08, 2017 (151)
18 GNOMAD ss2910868086 Nov 08, 2017 (151)
19 AFFY ss2984978076 Nov 08, 2017 (151)
20 ILLUMINA ss3021434858 Nov 08, 2017 (151)
21 ILLUMINA ss3626885692 Oct 12, 2018 (152)
22 ILLUMINA ss3626885693 Oct 12, 2018 (152)
23 ILLUMINA ss3634506876 Oct 12, 2018 (152)
24 ILLUMINA ss3640214210 Oct 12, 2018 (152)
25 ILLUMINA ss3644593459 Oct 12, 2018 (152)
26 ILLUMINA ss3651812272 Oct 12, 2018 (152)
27 ILLUMINA ss3653750443 Oct 12, 2018 (152)
28 ILLUMINA ss3725328688 Jul 13, 2019 (153)
29 ILLUMINA ss3744397036 Jul 13, 2019 (153)
30 ILLUMINA ss3744807550 Jul 13, 2019 (153)
31 EVA ss3750517405 Jul 13, 2019 (153)
32 PAGE_CC ss3771694104 Jul 13, 2019 (153)
33 ILLUMINA ss3772306997 Jul 13, 2019 (153)
34 KHV_HUMAN_GENOMES ss3815848223 Jul 13, 2019 (153)
35 KRGDB ss3926983294 Apr 27, 2020 (154)
36 KOGIC ss3972003929 Apr 27, 2020 (154)
37 EVA ss3984667478 Apr 26, 2021 (155)
38 TOPMED ss4919396130 Apr 26, 2021 (155)
39 TOMMO_GENOMICS ss5206470325 Apr 26, 2021 (155)
40 EVA ss5236906537 Apr 26, 2021 (155)
41 1000G_HIGH_COVERAGE ss5290922526 Oct 16, 2022 (156)
42 TRAN_CS_UWATERLOO ss5314435785 Oct 16, 2022 (156)
43 EVA ss5315623075 Oct 16, 2022 (156)
44 EVA ss5405834559 Oct 16, 2022 (156)
45 HUGCELL_USP ss5485660653 Oct 16, 2022 (156)
46 1000G_HIGH_COVERAGE ss5588461852 Oct 16, 2022 (156)
47 SANFORD_IMAGENETICS ss5653217528 Oct 16, 2022 (156)
48 TOMMO_GENOMICS ss5756307174 Oct 16, 2022 (156)
49 YY_MCH ss5813325814 Oct 16, 2022 (156)
50 EVA ss5847671605 Oct 16, 2022 (156)
51 EVA ss5850395108 Oct 16, 2022 (156)
52 EVA ss5904517868 Oct 16, 2022 (156)
53 EVA ss5944579821 Oct 16, 2022 (156)
54 1000Genomes NC_000012.11 - 56487560 Oct 12, 2018 (152)
55 1000Genomes_30x NC_000012.12 - 56093776 Oct 16, 2022 (156)
56 ExAC NC_000012.11 - 56487560 Oct 12, 2018 (152)
57 gnomAD - Genomes NC_000012.12 - 56093776 Apr 26, 2021 (155)
58 gnomAD - Exomes NC_000012.11 - 56487560 Jul 13, 2019 (153)
59 KOREAN population from KRGDB NC_000012.11 - 56487560 Apr 27, 2020 (154)
60 Korean Genome Project NC_000012.12 - 56093776 Apr 27, 2020 (154)
61 The PAGE Study NC_000012.12 - 56093776 Jul 13, 2019 (153)
62 CNV burdens in cranial meningiomas NC_000012.11 - 56487560 Apr 26, 2021 (155)
63 8.3KJPN NC_000012.11 - 56487560 Apr 26, 2021 (155)
64 14KJPN NC_000012.12 - 56093776 Oct 16, 2022 (156)
65 TopMed NC_000012.12 - 56093776 Apr 26, 2021 (155)
66 ALFA NC_000012.12 - 56093776 Apr 26, 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
ss281408661 NC_000012.10:54773826:A:T NC_000012.12:56093775:A:T (self)
57895052, 1256745, 9123765, 34160688, 216971, 64439632, ss337368359, ss491044665, ss491469462, ss534382934, ss780772829, ss783452567, ss1345141783, ss1690956035, ss1752073790, ss1917875021, ss1946340480, ss1959438391, ss1966651761, ss2739890947, ss2748889756, ss2910868086, ss2984978076, ss3021434858, ss3626885692, ss3626885693, ss3634506876, ss3640214210, ss3644593459, ss3651812272, ss3653750443, ss3744397036, ss3744807550, ss3750517405, ss3772306997, ss3926983294, ss3984667478, ss5206470325, ss5315623075, ss5405834559, ss5653217528, ss5847671605, ss5944579821 NC_000012.11:56487559:A:T NC_000012.12:56093775:A:T (self)
75987787, 408267169, 28381930, 915573, 90144278, 134941787, 68868735, ss2190042330, ss3725328688, ss3771694104, ss3815848223, ss3972003929, ss4919396130, ss5236906537, ss5290922526, ss5314435785, ss5485660653, ss5588461852, ss5756307174, ss5813325814, ss5850395108, ss5904517868 NC_000012.12:56093775:A:T NC_000012.12:56093775:A: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 rs146593760

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