11-128486082-C-T
Variant names:
Variant summary
Our verdict is Benign. The variant received -19 ACMG points: 0P and 19B. BP4_ModerateBP6_Very_StrongBP7BS1BS2
The NM_001143820.2(ETS1):c.600G>A(p.Ser200Ser) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00252 in 1,607,380 control chromosomes in the GnomAD database, including 75 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Genomes: 𝑓 0.0020 ( 2 hom., cov: 32)
Exomes 𝑓: 0.0026 ( 73 hom. )
Consequence
ETS1
NM_001143820.2 synonymous
NM_001143820.2 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.888
Publications
4 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 -19 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.21).
BP6
Variant 11-128486082-C-T is Benign according to our data. Variant chr11-128486082-C-T is described in ClinVar as [Benign]. Clinvar id is 777426.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BP7
Synonymous conserved (PhyloP=0.888 with no splicing effect.
BS1
Variant frequency is greater than expected in population sas. GnomAd4 allele frequency = 0.00198 (301/152052) while in subpopulation SAS AF = 0.0357 (172/4816). AF 95% confidence interval is 0.0314. There are 2 homozygotes in GnomAd4. There are 192 alleles in the male GnomAd4 subpopulation. Median coverage is 32. This position passed quality control check.
BS2
High AC in GnomAd4 at 301 Unknown,AD gene.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00198 AC: 301AN: 151934Hom.: 2 Cov.: 32 show subpopulations
GnomAD3 genomes
AF:
AC:
301
AN:
151934
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: 0.00471 AC: 1183AN: 251168 AF XY: 0.00633 show subpopulations
GnomAD2 exomes
AF:
AC:
1183
AN:
251168
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: 0.00258 AC: 3749AN: 1455328Hom.: 73 Cov.: 28 AF XY: 0.00356 AC XY: 2581AN XY: 724542 show subpopulations
GnomAD4 exome
AF:
AC:
3749
AN:
1455328
Hom.:
Cov.:
28
AF XY:
AC XY:
2581
AN XY:
724542
show subpopulations
African (AFR)
AF:
AC:
8
AN:
33330
American (AMR)
AF:
AC:
21
AN:
44676
Ashkenazi Jewish (ASJ)
AF:
AC:
145
AN:
26092
East Asian (EAS)
AF:
AC:
0
AN:
39644
South Asian (SAS)
AF:
AC:
2759
AN:
86028
European-Finnish (FIN)
AF:
AC:
1
AN:
53402
Middle Eastern (MID)
AF:
AC:
42
AN:
5754
European-Non Finnish (NFE)
AF:
AC:
598
AN:
1106228
Other (OTH)
AF:
AC:
175
AN:
60174
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.467
Heterozygous variant carriers
0
163
326
489
652
815
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
GnomAD4 genome AF: 0.00198 AC: 301AN: 152052Hom.: 2 Cov.: 32 AF XY: 0.00258 AC XY: 192AN XY: 74328 show subpopulations
GnomAD4 genome
AF:
AC:
301
AN:
152052
Hom.:
Cov.:
32
AF XY:
AC XY:
192
AN XY:
74328
show subpopulations
African (AFR)
AF:
AC:
6
AN:
41462
American (AMR)
AF:
AC:
17
AN:
15258
Ashkenazi Jewish (ASJ)
AF:
AC:
34
AN:
3468
East Asian (EAS)
AF:
AC:
0
AN:
5186
South Asian (SAS)
AF:
AC:
172
AN:
4816
European-Finnish (FIN)
AF:
AC:
0
AN:
10564
Middle Eastern (MID)
AF:
AC:
0
AN:
294
European-Non Finnish (NFE)
AF:
AC:
69
AN:
67986
Other (OTH)
AF:
AC:
3
AN:
2106
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.505
Heterozygous variant carriers
0
14
28
42
56
70
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Alfa
AF:
Hom.:
Bravo
AF:
Asia WGS
AF:
AC:
34
AN:
3478
EpiCase
AF:
EpiControl
AF:
ClinVar
Significance: 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:Benign
Review Status:criteria provided, single submitter
Collection Method:not provided
- -
Jul 31, 2018
Labcorp Genetics (formerly Invitae), Labcorp
Significance:Benign
Review Status:criteria provided, single submitter
Collection Method:clinical testing
- -
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
DANN
Benign
PhyloP100
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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