11-128489374-C-T
Variant names:
Variant summary
Our verdict is Benign. The variant received -16 ACMG points: 0P and 16B. BP4_StrongBP6_Very_StrongBS2
The NM_001143820.2(ETS1):c.451G>A(p.Ala151Thr) variant causes a missense change. The variant allele was found at a frequency of 0.00393 in 1,614,178 control chromosomes in the GnomAD database, including 18 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Genomes: 𝑓 0.0024 ( 0 hom., cov: 32)
Exomes 𝑓: 0.0041 ( 18 hom. )
Consequence
ETS1
NM_001143820.2 missense
NM_001143820.2 missense
Scores
1
6
12
Clinical Significance
Conservation
PhyloP100: 4.02
Publications
10 publications found
Genes affected
ETS1 (HGNC:3488): (ETS proto-oncogene 1, transcription factor) This gene encodes a member of the ETS family of transcription factors, which are defined by the presence of a conserved ETS DNA-binding domain that recognizes the core consensus DNA sequence GGAA/T in target genes. These proteins function either as transcriptional activators or repressors of numerous genes, and are involved in stem cell development, cell senescence and death, and tumorigenesis. Alternatively spliced transcript variants encoding different isoforms have been described for this gene.[provided by RefSeq, Jul 2011]
ETS1 Gene-Disease associations (from GenCC):
- congenital heart diseaseInheritance: AD Classification: MODERATE Submitted by: ClinGen
- systemic lupus erythematosusInheritance: Unknown Classification: SUPPORTIVE Submitted by: Orphanet
- Tourette syndromeInheritance: Unknown Classification: NO_KNOWN Submitted by: Labcorp Genetics (formerly Invitae)
Genome browser will be placed here
ACMG classification
Classification was made for transcript
Our verdict: Benign. The variant received -16 ACMG points.
BP4
Computational evidence support a benign effect (MetaRNN=0.012863308).
BP6
Variant 11-128489374-C-T is Benign according to our data. Variant chr11-128489374-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 779438.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BS2
High AC in GnomAd4 at 369 Unknown,AD gene.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00243 AC: 370AN: 152198Hom.: 0 Cov.: 32 show subpopulations
GnomAD3 genomes
AF:
AC:
370
AN:
152198
Hom.:
Cov.:
32
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
GnomAD2 exomes AF: 0.00215 AC: 541AN: 251382 AF XY: 0.00230 show subpopulations
GnomAD2 exomes
AF:
AC:
541
AN:
251382
AF XY:
Gnomad AFR exome
AF:
Gnomad AMR exome
AF:
Gnomad ASJ exome
AF:
Gnomad EAS exome
AF:
Gnomad FIN exome
AF:
Gnomad NFE exome
AF:
Gnomad OTH exome
AF:
GnomAD4 exome AF: 0.00409 AC: 5974AN: 1461862Hom.: 18 Cov.: 32 AF XY: 0.00397 AC XY: 2889AN XY: 727240 show subpopulations
GnomAD4 exome
AF:
AC:
5974
AN:
1461862
Hom.:
Cov.:
32
AF XY:
AC XY:
2889
AN XY:
727240
show subpopulations
African (AFR)
AF:
AC:
24
AN:
33480
American (AMR)
AF:
AC:
45
AN:
44724
Ashkenazi Jewish (ASJ)
AF:
AC:
3
AN:
26136
East Asian (EAS)
AF:
AC:
1
AN:
39700
South Asian (SAS)
AF:
AC:
80
AN:
86258
European-Finnish (FIN)
AF:
AC:
31
AN:
53420
Middle Eastern (MID)
AF:
AC:
4
AN:
5768
European-Non Finnish (NFE)
AF:
AC:
5579
AN:
1111984
Other (OTH)
AF:
AC:
207
AN:
60392
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.456
Heterozygous variant carriers
0
307
614
920
1227
1534
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
GnomAD4 genome AF: 0.00242 AC: 369AN: 152316Hom.: 0 Cov.: 32 AF XY: 0.00218 AC XY: 162AN XY: 74470 show subpopulations
GnomAD4 genome
AF:
AC:
369
AN:
152316
Hom.:
Cov.:
32
AF XY:
AC XY:
162
AN XY:
74470
show subpopulations
African (AFR)
AF:
AC:
37
AN:
41580
American (AMR)
AF:
AC:
24
AN:
15304
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
3470
East Asian (EAS)
AF:
AC:
0
AN:
5186
South Asian (SAS)
AF:
AC:
3
AN:
4828
European-Finnish (FIN)
AF:
AC:
7
AN:
10618
Middle Eastern (MID)
AF:
AC:
0
AN:
294
European-Non Finnish (NFE)
AF:
AC:
293
AN:
68016
Other (OTH)
AF:
AC:
5
AN:
2108
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.500
Heterozygous variant carriers
0
19
37
56
74
93
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Alfa
AF:
Hom.:
Bravo
AF:
TwinsUK
AF:
AC:
21
ALSPAC
AF:
AC:
22
ESP6500AA
AF:
AC:
2
ESP6500EA
AF:
AC:
37
ExAC
AF:
AC:
280
Asia WGS
AF:
AC:
4
AN:
3478
EpiCase
AF:
EpiControl
AF:
ClinVar
Significance: Likely benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not provided Benign:2
-
Breakthrough Genomics, Breakthrough Genomics
Significance:Likely benign
Review Status:criteria provided, single submitter
Collection Method:not provided
- -
Dec 31, 2019
Labcorp Genetics (formerly Invitae), Labcorp
Significance:Likely benign
Review Status:criteria provided, single submitter
Collection Method:clinical testing
- -
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
DANN
Uncertain
DEOGEN2
Benign
.;.;.;T
Eigen
Uncertain
Eigen_PC
Uncertain
FATHMM_MKL
Pathogenic
D
LIST_S2
Uncertain
D;D;D;D
M_CAP
Benign
T
MetaRNN
Benign
T;T;T;T
MetaSVM
Benign
T
MutationAssessor
Uncertain
.;M;M;M
PhyloP100
PrimateAI
Uncertain
T
PROVEAN
Benign
N;N;N;N
REVEL
Benign
Sift
Benign
T;T;T;T
Sift4G
Benign
T;T;T;T
Polyphen
0.47
.;.;.;P
Vest4
MVP
MPC
ClinPred
T
GERP RS
Varity_R
gMVP
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
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