chr12-11650174-C-T
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Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBS1BS2
The NM_001987.5(ETV6):c.33+14C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000813 in 1,611,408 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 0.000059 ( 0 hom., cov: 31)
Exomes 𝑓: 0.000084 ( 0 hom. )
Consequence
ETV6
NM_001987.5 intron
NM_001987.5 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.644
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 -14 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.64).
BP6
Variant 12-11650174-C-T is Benign according to our data. Variant chr12-11650174-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 2973362.Status of the report is criteria_provided_single_submitter, 1 stars.
BS1
Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.0000592 (9/152004) while in subpopulation NFE AF= 0.000103 (7/67982). AF 95% confidence interval is 0.0000477. There are 0 homozygotes in gnomad4. There are 5 alleles in male gnomad4 subpopulation. Median coverage is 31. This position pass quality control queck.
BS2
High AC in GnomAd4 at 9 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ETV6 | NM_001987.5 | c.33+14C>T | intron_variant | ENST00000396373.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ETV6 | ENST00000396373.9 | c.33+14C>T | intron_variant | 1 | NM_001987.5 | P1 | |||
ETV6 | ENST00000541426.1 | n.217+14C>T | intron_variant, non_coding_transcript_variant | 4 | |||||
ETV6 | ENST00000544715.1 | n.150+14C>T | intron_variant, non_coding_transcript_variant | 3 |
Frequencies
GnomAD3 genomes AF: 0.0000592 AC: 9AN: 152004Hom.: 0 Cov.: 31
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GnomAD3 exomes AF: 0.0000441 AC: 11AN: 249414Hom.: 0 AF XY: 0.0000740 AC XY: 10AN XY: 135074
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GnomAD4 exome AF: 0.0000836 AC: 122AN: 1459404Hom.: 0 Cov.: 29 AF XY: 0.0000771 AC XY: 56AN XY: 726222
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GnomAD4 genome AF: 0.0000592 AC: 9AN: 152004Hom.: 0 Cov.: 31 AF XY: 0.0000673 AC XY: 5AN XY: 74276
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Sep 08, 2023 | - - |
Computational scores
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Name
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at