chr12-11650170-T-A
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Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The NM_001987.5(ETV6):c.33+10T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000676 in 1,611,970 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Genomes: 𝑓 0.000053 ( 0 hom., cov: 31)
Exomes 𝑓: 0.000069 ( 0 hom. )
Consequence
ETV6
NM_001987.5 intron
NM_001987.5 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.0750
Genes affected
ETV6 (HGNC:3495): (ETS variant transcription factor 6) This gene encodes an ETS family transcription factor. The product of this gene contains two functional domains: a N-terminal pointed (PNT) domain that is involved in protein-protein interactions with itself and other proteins, and a C-terminal DNA-binding domain. Gene knockout studies in mice suggest that it is required for hematopoiesis and maintenance of the developing vascular network. This gene is known to be involved in a large number of chromosomal rearrangements associated with leukemia and congenital fibrosarcoma. [provided by RefSeq, Sep 2008]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -20 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.65).
BP6
Variant 12-11650170-T-A is Benign according to our data. Variant chr12-11650170-T-A is described in ClinVar as [Likely_benign]. Clinvar id is 2063751.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BS1
Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.0000527 (8/151942) while in subpopulation NFE AF= 0.000118 (8/67972). AF 95% confidence interval is 0.0000585. There are 0 homozygotes in gnomad4. There are 3 alleles in male gnomad4 subpopulation. Median coverage is 31. This position pass quality control queck.
BS2
High AC in GnomAd4 at 8 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ETV6 | NM_001987.5 | c.33+10T>A | intron_variant | ENST00000396373.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ETV6 | ENST00000396373.9 | c.33+10T>A | intron_variant | 1 | NM_001987.5 | P1 | |||
ETV6 | ENST00000541426.1 | n.217+10T>A | intron_variant, non_coding_transcript_variant | 4 | |||||
ETV6 | ENST00000544715.1 | n.150+10T>A | intron_variant, non_coding_transcript_variant | 3 |
Frequencies
GnomAD3 genomes AF: 0.0000527 AC: 8AN: 151942Hom.: 0 Cov.: 31
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GnomAD3 exomes AF: 0.0000681 AC: 17AN: 249498Hom.: 0 AF XY: 0.0000370 AC XY: 5AN XY: 135108
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GnomAD4 exome AF: 0.0000692 AC: 101AN: 1460028Hom.: 0 Cov.: 29 AF XY: 0.0000661 AC XY: 48AN XY: 726442
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GnomAD4 genome AF: 0.0000527 AC: 8AN: 151942Hom.: 0 Cov.: 31 AF XY: 0.0000404 AC XY: 3AN XY: 74208
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ClinVar
Significance: Likely benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
ETV6-related disorder Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Dec 28, 2023 | This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Mar 20, 2023 | - - |
Computational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
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