Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation

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.

rs147790742

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr11:121118487 (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
G>C
Variation Type
SNV Single Nucleotide Variation
Frequency
C=0.002561 (678/264690, TOPMED)
C=0.000585 (147/251476, GnomAD_exome)
C=0.002709 (380/140260, GnomAD) (+ 7 more)
C=0.000782 (95/121410, ExAC)
C=0.00060 (27/44790, ALFA)
C=0.00215 (28/13004, GO-ESP)
C=0.0033 (21/6404, 1000G_30x)
C=0.0028 (14/5008, 1000G)
G=0.5 (2/4, SGDP_PRJ)
C=0.5 (2/4, SGDP_PRJ)
Clinical Significance
Reported in ClinVar
Gene : Consequence
TBCEL-TECTA : Synonymous Variant
TECTA : Synonymous 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 44790 G=0.99940 C=0.00060
European Sub 32784 G=1.00000 C=0.00000
African Sub 3560 G=0.9935 C=0.0065
African Others Sub 122 G=0.975 C=0.025
African American Sub 3438 G=0.9942 C=0.0058
Asian Sub 168 G=1.000 C=0.000
East Asian Sub 112 G=1.000 C=0.000
Other Asian Sub 56 G=1.00 C=0.00
Latin American 1 Sub 500 G=1.000 C=0.000
Latin American 2 Sub 628 G=1.000 C=0.000
South Asian Sub 98 G=1.00 C=0.00
Other Sub 7052 G=0.9994 C=0.0006


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 G=0.997439 C=0.002561
gnomAD - Exomes Global Study-wide 251476 G=0.999415 C=0.000585
gnomAD - Exomes European Sub 135398 G=0.999993 C=0.000007
gnomAD - Exomes Asian Sub 49010 G=1.00000 C=0.00000
gnomAD - Exomes American Sub 34592 G=0.99971 C=0.00029
gnomAD - Exomes African Sub 16256 G=0.99170 C=0.00830
gnomAD - Exomes Ashkenazi Jewish Sub 10080 G=1.00000 C=0.00000
gnomAD - Exomes Other Sub 6140 G=0.9998 C=0.0002
gnomAD - Genomes Global Study-wide 140260 G=0.997291 C=0.002709
gnomAD - Genomes European Sub 75954 G=0.99999 C=0.00001
gnomAD - Genomes African Sub 42040 G=0.99151 C=0.00849
gnomAD - Genomes American Sub 13660 G=0.99876 C=0.00124
gnomAD - Genomes Ashkenazi Jewish Sub 3320 G=1.0000 C=0.0000
gnomAD - Genomes East Asian Sub 3132 G=1.0000 C=0.0000
gnomAD - Genomes Other Sub 2154 G=0.9977 C=0.0023
ExAC Global Study-wide 121410 G=0.999218 C=0.000782
ExAC Europe Sub 73352 G=0.99999 C=0.00001
ExAC Asian Sub 25166 G=1.00000 C=0.00000
ExAC American Sub 11578 G=0.99983 C=0.00017
ExAC African Sub 10406 G=0.99116 C=0.00884
ExAC Other Sub 908 G=1.000 C=0.000
Allele Frequency Aggregator Total Global 44790 G=0.99940 C=0.00060
Allele Frequency Aggregator European Sub 32784 G=1.00000 C=0.00000
Allele Frequency Aggregator Other Sub 7052 G=0.9994 C=0.0006
Allele Frequency Aggregator African Sub 3560 G=0.9935 C=0.0065
Allele Frequency Aggregator Latin American 2 Sub 628 G=1.000 C=0.000
Allele Frequency Aggregator Latin American 1 Sub 500 G=1.000 C=0.000
Allele Frequency Aggregator Asian Sub 168 G=1.000 C=0.000
Allele Frequency Aggregator South Asian Sub 98 G=1.00 C=0.00
GO Exome Sequencing Project Global Study-wide 13004 G=0.99785 C=0.00215
GO Exome Sequencing Project European American Sub 8598 G=0.9999 C=0.0001
GO Exome Sequencing Project African American Sub 4406 G=0.9939 C=0.0061
1000Genomes_30x Global Study-wide 6404 G=0.9967 C=0.0033
1000Genomes_30x African Sub 1786 G=0.9882 C=0.0118
1000Genomes_30x Europe Sub 1266 G=1.0000 C=0.0000
1000Genomes_30x South Asian Sub 1202 G=1.0000 C=0.0000
1000Genomes_30x East Asian Sub 1170 G=1.0000 C=0.0000
1000Genomes_30x American Sub 980 G=1.000 C=0.000
1000Genomes Global Study-wide 5008 G=0.9972 C=0.0028
1000Genomes African Sub 1322 G=0.9894 C=0.0106
1000Genomes East Asian Sub 1008 G=1.0000 C=0.0000
1000Genomes Europe Sub 1006 G=1.0000 C=0.0000
1000Genomes South Asian Sub 978 G=1.000 C=0.000
1000Genomes American Sub 694 G=1.000 C=0.000
SGDP_PRJ Global Study-wide 4 G=0.5 C=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 11 NC_000011.10:g.121118487G>C
GRCh37.p13 chr 11 NC_000011.9:g.120989196G>C
TECTA RefSeqGene NG_011633.1:g.20822G>C
Gene: TECTA, tectorin alpha (plus strand)
Molecule type Change Amino acid[Codon] SO Term
TECTA transcript NM_005422.4:c.972G>C V [GTG] > V [GTC] Coding Sequence Variant
alpha-tectorin precursor NP_005413.2:p.Val324= V (Val) > V (Val) Synonymous Variant
Gene: TBCEL-TECTA, TBCEL-TECTA readthrough (plus strand)
Molecule type Change Amino acid[Codon] SO Term
TBCEL-TECTA transcript NM_001378761.1:c.1929G>C V [GTG] > V [GTC] Coding Sequence Variant
TBCEL-TECTA protein NP_001365690.1:p.Val643= V (Val) > V (Val) Synonymous 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: C (allele ID: 273542 )
ClinVar Accession Disease Names Clinical Significance
RCV000261652.7 not specified Benign-Likely-Benign
RCV000287283.3 Autosomal dominant nonsyndromic hearing loss 12 Benign
RCV000321313.3 Autosomal recessive nonsyndromic hearing loss 21 Uncertain-Significance
RCV000713815.8 not provided Benign-Likely-Benign
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 G= C
GRCh38.p14 chr 11 NC_000011.10:g.121118487= NC_000011.10:g.121118487G>C
GRCh37.p13 chr 11 NC_000011.9:g.120989196= NC_000011.9:g.120989196G>C
TECTA RefSeqGene NG_011633.1:g.20822= NG_011633.1:g.20822G>C
TECTA transcript NM_005422.4:c.972= NM_005422.4:c.972G>C
TECTA transcript NM_005422.3:c.972= NM_005422.3:c.972G>C
TECTA transcript NM_005422.2:c.972= NM_005422.2:c.972G>C
TBCEL-TECTA transcript NM_001378761.1:c.1929= NM_001378761.1:c.1929G>C
alpha-tectorin precursor NP_005413.2:p.Val324= NP_005413.2:p.Val324=
TBCEL-TECTA protein NP_001365690.1:p.Val643= NP_001365690.1:p.Val643=
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#.

20 SubSNP, 9 Frequency, 4 ClinVar submissions
No Submitter Submission ID Date (Build)
1 NHLBI-ESP ss342343118 May 09, 2011 (134)
2 1000GENOMES ss462579011 Sep 17, 2011 (135)
3 1000GENOMES ss491031348 May 04, 2012 (137)
4 1000GENOMES ss1343247984 Aug 21, 2014 (142)
5 EVA_EXAC ss1690679712 Apr 01, 2015 (144)
6 HUMAN_LONGEVITY ss2186291238 Dec 20, 2016 (150)
7 GNOMAD ss2739462060 Nov 08, 2017 (151)
8 GNOMAD ss2748761430 Nov 08, 2017 (151)
9 GNOMAD ss2905247762 Nov 08, 2017 (151)
10 EVA ss3824681413 Apr 26, 2020 (154)
11 SGDP_PRJ ss3877282663 Apr 26, 2020 (154)
12 EVA ss3986549339 Apr 26, 2021 (155)
13 TOPMED ss4902403706 Apr 26, 2021 (155)
14 1000G_HIGH_COVERAGE ss5289145282 Oct 16, 2022 (156)
15 EVA ss5402699829 Oct 16, 2022 (156)
16 HUGCELL_USP ss5484110510 Oct 16, 2022 (156)
17 1000G_HIGH_COVERAGE ss5585752118 Oct 16, 2022 (156)
18 SANFORD_IMAGENETICS ss5652210607 Oct 16, 2022 (156)
19 EVA ss5921944261 Oct 16, 2022 (156)
20 EVA ss5943547713 Oct 16, 2022 (156)
21 1000Genomes NC_000011.9 - 120989196 Oct 12, 2018 (152)
22 1000Genomes_30x NC_000011.10 - 121118487 Oct 16, 2022 (156)
23 ExAC NC_000011.9 - 120989196 Oct 12, 2018 (152)
24 gnomAD - Genomes NC_000011.10 - 121118487 Apr 26, 2021 (155)
25 gnomAD - Exomes NC_000011.9 - 120989196 Jul 13, 2019 (153)
26 GO Exome Sequencing Project NC_000011.9 - 120989196 Oct 12, 2018 (152)
27 SGDP_PRJ NC_000011.9 - 120989196 Apr 26, 2020 (154)
28 TopMed NC_000011.10 - 121118487 Apr 26, 2021 (155)
29 ALFA NC_000011.10 - 121118487 Apr 26, 2021 (155)
30 ClinVar RCV000261652.7 Oct 16, 2022 (156)
31 ClinVar RCV000287283.3 Oct 16, 2022 (156)
32 ClinVar RCV000321313.3 Oct 16, 2022 (156)
33 ClinVar RCV000713815.8 Oct 16, 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
55840133, 959085, 8682990, 1138932, 29299643, ss342343118, ss462579011, ss491031348, ss1343247984, ss1690679712, ss2739462060, ss2748761430, ss2905247762, ss3824681413, ss3877282663, ss3986549339, ss5402699829, ss5652210607, ss5943547713 NC_000011.9:120989195:G:C NC_000011.10:121118486:G:C (self)
RCV000261652.7, RCV000287283.3, RCV000321313.3, RCV000713815.8, 73278053, 393981885, 117949362, 668854018, ss2186291238, ss4902403706, ss5289145282, ss5484110510, ss5585752118, ss5921944261 NC_000011.10:121118486:G:C NC_000011.10:121118486:G:C (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 rs147790742

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