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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.

rs149743004

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr12:3017525 (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>A
Variation Type
SNV Single Nucleotide Variation
Frequency
A=0.001024 (271/264690, TOPMED)
A=0.001508 (370/245346, GnomAD_exome)
A=0.001255 (176/140288, GnomAD) (+ 10 more)
A=0.001750 (223/127426, ALFA)
A=0.001962 (197/100394, ExAC)
A=0.00154 (20/13002, GO-ESP)
A=0.0005 (3/6404, 1000G_30x)
A=0.0006 (3/5008, 1000G)
A=0.0045 (20/4480, Estonian)
A=0.0013 (5/3854, ALSPAC)
A=0.0011 (4/3708, TWINSUK)
A=0.003 (3/998, GoNL)
A=0.03 (1/40, GENOME_DK)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
TEAD4 : 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 143628 G=0.998252 A=0.001748
European Sub 119344 G=0.998090 A=0.001910
African Sub 8498 G=0.9994 A=0.0006
African Others Sub 308 G=1.000 A=0.000
African American Sub 8190 G=0.9994 A=0.0006
Asian Sub 194 G=1.000 A=0.000
East Asian Sub 112 G=1.000 A=0.000
Other Asian Sub 82 G=1.00 A=0.00
Latin American 1 Sub 500 G=0.998 A=0.002
Latin American 2 Sub 648 G=1.000 A=0.000
South Asian Sub 98 G=1.00 A=0.00
Other Sub 14346 G=0.99882 A=0.00118


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=0.998976 A=0.001024
gnomAD - Exomes Global Study-wide 245346 G=0.998492 A=0.001508
gnomAD - Exomes European Sub 131448 G=0.998144 A=0.001856
gnomAD - Exomes Asian Sub 48370 G=0.99806 A=0.00194
gnomAD - Exomes American Sub 34100 G=0.99938 A=0.00062
gnomAD - Exomes African Sub 15562 G=0.99955 A=0.00045
gnomAD - Exomes Ashkenazi Jewish Sub 9898 G=0.9999 A=0.0001
gnomAD - Exomes Other Sub 5968 G=0.9995 A=0.0005
gnomAD - Genomes Global Study-wide 140288 G=0.998745 A=0.001255
gnomAD - Genomes European Sub 75956 G=0.99795 A=0.00205
gnomAD - Genomes African Sub 42060 G=0.99971 A=0.00029
gnomAD - Genomes American Sub 13666 G=0.99971 A=0.00029
gnomAD - Genomes Ashkenazi Jewish Sub 3324 G=1.0000 A=0.0000
gnomAD - Genomes East Asian Sub 3132 G=1.0000 A=0.0000
gnomAD - Genomes Other Sub 2150 G=0.9981 A=0.0019
Allele Frequency Aggregator Total Global 127426 G=0.998250 A=0.001750
Allele Frequency Aggregator European Sub 109364 G=0.998144 A=0.001856
Allele Frequency Aggregator Other Sub 12934 G=0.99869 A=0.00131
Allele Frequency Aggregator African Sub 3688 G=0.9995 A=0.0005
Allele Frequency Aggregator Latin American 2 Sub 648 G=1.000 A=0.000
Allele Frequency Aggregator Latin American 1 Sub 500 G=0.998 A=0.002
Allele Frequency Aggregator Asian Sub 194 G=1.000 A=0.000
Allele Frequency Aggregator South Asian Sub 98 G=1.00 A=0.00
ExAC Global Study-wide 100394 G=0.998038 A=0.001962
ExAC Europe Sub 60458 G=0.99783 A=0.00217
ExAC Asian Sub 21336 G=0.99775 A=0.00225
ExAC American Sub 9652 G=0.9990 A=0.0010
ExAC African Sub 8198 G=0.9994 A=0.0006
ExAC Other Sub 750 G=0.996 A=0.004
GO Exome Sequencing Project Global Study-wide 13002 G=0.99846 A=0.00154
GO Exome Sequencing Project European American Sub 8600 G=0.9979 A=0.0021
GO Exome Sequencing Project African American Sub 4402 G=0.9995 A=0.0005
1000Genomes_30x Global Study-wide 6404 G=0.9995 A=0.0005
1000Genomes_30x African Sub 1786 G=1.0000 A=0.0000
1000Genomes_30x Europe Sub 1266 G=0.9984 A=0.0016
1000Genomes_30x South Asian Sub 1202 G=1.0000 A=0.0000
1000Genomes_30x East Asian Sub 1170 G=1.0000 A=0.0000
1000Genomes_30x American Sub 980 G=0.999 A=0.001
1000Genomes Global Study-wide 5008 G=0.9994 A=0.0006
1000Genomes African Sub 1322 G=1.0000 A=0.0000
1000Genomes East Asian Sub 1008 G=1.0000 A=0.0000
1000Genomes Europe Sub 1006 G=0.9980 A=0.0020
1000Genomes South Asian Sub 978 G=1.000 A=0.000
1000Genomes American Sub 694 G=0.999 A=0.001
Genetic variation in the Estonian population Estonian Study-wide 4480 G=0.9955 A=0.0045
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 G=0.9987 A=0.0013
UK 10K study - Twins TWIN COHORT Study-wide 3708 G=0.9989 A=0.0011
Genome of the Netherlands Release 5 Genome of the Netherlands Study-wide 998 G=0.997 A=0.003
The Danish reference pan genome Danish Study-wide 40 G=0.97 A=0.03
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.3017525G>A
GRCh37.p13 chr 12 NC_000012.11:g.3126691G>A
TEAD4 RefSeqGene NG_029958.1:g.63214G>A
Gene: TEAD4, TEA domain transcription factor 4 (plus strand)
Molecule type Change Amino acid[Codon] SO Term
TEAD4 transcript variant 2 NM_201441.3:c.355-1020G>A N/A Intron Variant
TEAD4 transcript variant 1 NM_003213.4:c.482G>A G [GGG] > E [GAG] Coding Sequence Variant
transcriptional enhancer factor TEF-3 isoform 1 NP_003204.2:p.Gly161Glu G (Gly) > E (Glu) Missense Variant
TEAD4 transcript variant 3 NM_201443.3:c.95G>A G [GGG] > E [GAG] Coding Sequence Variant
transcriptional enhancer factor TEF-3 isoform 3 NP_958851.1:p.Gly32Glu G (Gly) > E (Glu) 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 G= A
GRCh38.p14 chr 12 NC_000012.12:g.3017525= NC_000012.12:g.3017525G>A
GRCh37.p13 chr 12 NC_000012.11:g.3126691= NC_000012.11:g.3126691G>A
TEAD4 RefSeqGene NG_029958.1:g.63214= NG_029958.1:g.63214G>A
TEAD4 transcript variant 1 NM_003213.4:c.482= NM_003213.4:c.482G>A
TEAD4 transcript variant 1 NM_003213.3:c.482= NM_003213.3:c.482G>A
TEAD4 transcript variant 3 NM_201443.3:c.95= NM_201443.3:c.95G>A
TEAD4 transcript variant 3 NM_201443.2:c.95= NM_201443.2:c.95G>A
transcriptional enhancer factor TEF-3 isoform 1 NP_003204.2:p.Gly161= NP_003204.2:p.Gly161Glu
transcriptional enhancer factor TEF-3 isoform 3 NP_958851.1:p.Gly32= NP_958851.1:p.Gly32Glu
TEAD4 transcript variant 2 NM_201441.2:c.355-1020= NM_201441.2:c.355-1020G>A
TEAD4 transcript variant 2 NM_201441.3:c.355-1020= NM_201441.3:c.355-1020G>A
TEAD4 transcript variant X2 XM_005253756.1:c.436-1020= XM_005253756.1:c.436-1020G>A
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#.

45 SubSNP, 13 Frequency submissions
No Submitter Submission ID Date (Build)
1 NHLBI-ESP ss342346898 May 09, 2011 (134)
2 1000GENOMES ss462658984 Sep 17, 2011 (135)
3 1000GENOMES ss491034455 May 04, 2012 (137)
4 EXOME_CHIP ss491462629 May 04, 2012 (137)
5 ILLUMINA ss783594207 Sep 08, 2015 (146)
6 EVA-GONL ss989173740 Aug 21, 2014 (142)
7 1000GENOMES ss1343762604 Aug 21, 2014 (142)
8 EVA_GENOME_DK ss1576075527 Apr 01, 2015 (144)
9 EVA_DECODE ss1598844954 Apr 01, 2015 (144)
10 EVA_UK10K_ALSPAC ss1627894037 Apr 01, 2015 (144)
11 EVA_UK10K_TWINSUK ss1670888070 Apr 01, 2015 (144)
12 EVA_EXAC ss1690742208 Apr 01, 2015 (144)
13 ILLUMINA ss1752064387 Sep 08, 2015 (146)
14 ILLUMINA ss1917869447 Feb 12, 2016 (147)
15 ILLUMINA ss1946329028 Feb 12, 2016 (147)
16 ILLUMINA ss1959406485 Feb 12, 2016 (147)
17 JJLAB ss2027014141 Sep 14, 2016 (149)
18 HUMAN_LONGEVITY ss2187330967 Dec 20, 2016 (150)
19 GNOMAD ss2739557849 Nov 08, 2017 (151)
20 GNOMAD ss2748790774 Nov 08, 2017 (151)
21 GNOMAD ss2906666725 Nov 08, 2017 (151)
22 AFFY ss2984964950 Nov 08, 2017 (151)
23 SWEGEN ss3009101552 Nov 08, 2017 (151)
24 ILLUMINA ss3021399030 Nov 08, 2017 (151)
25 ILLUMINA ss3634486940 Oct 12, 2018 (152)
26 ILLUMINA ss3640194275 Oct 12, 2018 (152)
27 ILLUMINA ss3644581964 Oct 12, 2018 (152)
28 ILLUMINA ss3651770772 Oct 12, 2018 (152)
29 ILLUMINA ss3653737187 Oct 12, 2018 (152)
30 EGCUT_WGS ss3676432286 Jul 13, 2019 (153)
31 EVA_DECODE ss3692991751 Jul 13, 2019 (153)
32 ILLUMINA ss3744390698 Jul 13, 2019 (153)
33 ILLUMINA ss3744787673 Jul 13, 2019 (153)
34 ILLUMINA ss3772287284 Jul 13, 2019 (153)
35 EVA ss3824694809 Apr 26, 2020 (154)
36 TOPMED ss4906695486 Apr 27, 2021 (155)
37 1000G_HIGH_COVERAGE ss5289593232 Oct 17, 2022 (156)
38 EVA ss5403537923 Oct 17, 2022 (156)
39 HUGCELL_USP ss5484509153 Oct 17, 2022 (156)
40 1000G_HIGH_COVERAGE ss5586416871 Oct 17, 2022 (156)
41 EVA ss5837503102 Oct 17, 2022 (156)
42 EVA ss5847657224 Oct 17, 2022 (156)
43 EVA ss5848343102 Oct 17, 2022 (156)
44 EVA ss5903049802 Oct 17, 2022 (156)
45 EVA ss5943815301 Oct 17, 2022 (156)
46 1000Genomes NC_000012.11 - 3126691 Oct 12, 2018 (152)
47 1000Genomes_30x NC_000012.12 - 3017525 Oct 17, 2022 (156)
48 The Avon Longitudinal Study of Parents and Children NC_000012.11 - 3126691 Oct 12, 2018 (152)
49 Genetic variation in the Estonian population NC_000012.11 - 3126691 Oct 12, 2018 (152)
50 ExAC NC_000012.11 - 3126691 Oct 12, 2018 (152)
51 The Danish reference pan genome NC_000012.11 - 3126691 Apr 26, 2020 (154)
52 gnomAD - Genomes NC_000012.12 - 3017525 Apr 27, 2021 (155)
53 gnomAD - Exomes NC_000012.11 - 3126691 Jul 13, 2019 (153)
54 GO Exome Sequencing Project NC_000012.11 - 3126691 Oct 12, 2018 (152)
55 Genome of the Netherlands Release 5 NC_000012.11 - 3126691 Apr 26, 2020 (154)
56 TopMed NC_000012.12 - 3017525 Apr 27, 2021 (155)
57 UK 10K study - Twins NC_000012.11 - 3126691 Oct 12, 2018 (152)
58 ALFA NC_000012.12 - 3017525 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
ss1598844954 NC_000012.10:2996951:G:A NC_000012.12:3017524:G:A (self)
56372514, 31305079, 22170534, 1025932, 2817410, 8781507, 1152317, 13965306, 31305079, ss342346898, ss462658984, ss491034455, ss491462629, ss783594207, ss989173740, ss1343762604, ss1576075527, ss1627894037, ss1670888070, ss1690742208, ss1752064387, ss1917869447, ss1946329028, ss1959406485, ss2027014141, ss2739557849, ss2748790774, ss2906666725, ss2984964950, ss3009101552, ss3021399030, ss3634486940, ss3640194275, ss3644581964, ss3651770772, ss3653737187, ss3676432286, ss3744390698, ss3744787673, ss3772287284, ss3824694809, ss5403537923, ss5837503102, ss5847657224, ss5848343102, ss5943815301 NC_000012.11:3126690:G:A NC_000012.12:3017524:G:A (self)
73942806, 397573922, 122241143, 1074959981, ss2187330967, ss3692991751, ss4906695486, ss5289593232, ss5484509153, ss5586416871, ss5903049802 NC_000012.12:3017524:G:A NC_000012.12:3017524:G:A (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 rs149743004

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