NM_001143820.2:c.921C>T
Variant names:
Variant summary
Our verdict is Benign. Variant got -17 ACMG points: 0P and 17B. BP4_StrongBP6_Very_StrongBP7BS2
The NM_001143820.2(ETS1):c.921C>T(p.Arg307Arg) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00946 in 1,614,070 control chromosomes in the GnomAD database, including 90 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Genomes: 𝑓 0.0070 ( 9 hom., cov: 31)
Exomes 𝑓: 0.0097 ( 81 hom. )
Consequence
ETS1
NM_001143820.2 synonymous
NM_001143820.2 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.332
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]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -17 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.47).
BP6
Variant 11-128480393-G-A is Benign according to our data. Variant chr11-128480393-G-A is described in ClinVar as [Benign]. Clinvar id is 715411.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BP7
Synonymous conserved (PhyloP=-0.332 with no splicing effect.
BS2
High AC in GnomAd4 at 1058 AD gene.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00696 AC: 1059AN: 152098Hom.: 9 Cov.: 31
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GnomAD3 exomes AF: 0.00718 AC: 1802AN: 250942Hom.: 7 AF XY: 0.00753 AC XY: 1021AN XY: 135602
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GnomAD4 exome AF: 0.00972 AC: 14214AN: 1461854Hom.: 81 Cov.: 33 AF XY: 0.00979 AC XY: 7123AN XY: 727228
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GnomAD4 genome AF: 0.00695 AC: 1058AN: 152216Hom.: 9 Cov.: 31 AF XY: 0.00619 AC XY: 461AN XY: 74424
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ClinVar
Significance: Benign
Submissions summary: Benign:3
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not provided Benign:3
Dec 01, 2024
CeGaT Center for Human Genetics Tuebingen
Significance: Benign
Review Status: criteria provided, single submitter
Collection Method: clinical testing
ETS1: BP4, BS1, BS2 -
Dec 31, 2019
Labcorp Genetics (formerly Invitae), Labcorp
Significance: Benign
Review Status: criteria provided, single submitter
Collection Method: clinical testing
- -
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Breakthrough Genomics, Breakthrough Genomics
Significance: Benign
Review Status: criteria provided, single submitter
Collection Method: not provided
- -
Computational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at