rs201196326
Variant summary
Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP6BS1BS2
The NM_001987.5(ETV6):c.1152+5A>G variant causes a splice donor 5th base, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000256 in 1,614,052 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Consequence
NM_001987.5 splice_donor_5th_base, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -13 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ETV6 | NM_001987.5 | c.1152+5A>G | splice_donor_5th_base_variant, intron_variant | ENST00000396373.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ETV6 | ENST00000396373.9 | c.1152+5A>G | splice_donor_5th_base_variant, intron_variant | 1 | NM_001987.5 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.000815 AC: 124AN: 152198Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000287 AC: 72AN: 251100Hom.: 0 AF XY: 0.000258 AC XY: 35AN XY: 135730
GnomAD4 exome AF: 0.000198 AC: 290AN: 1461736Hom.: 0 Cov.: 31 AF XY: 0.000215 AC XY: 156AN XY: 727168
GnomAD4 genome ? AF: 0.000814 AC: 124AN: 152316Hom.: 0 Cov.: 32 AF XY: 0.000752 AC XY: 56AN XY: 74472
ClinVar
Submissions by phenotype
Thrombocytopenia 5 Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Baylor Genetics | Jan 13, 2019 | This variant was determined to be of uncertain significance according to ACMG Guidelines, 2015 [PMID:25741868]. - |
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Genetic Services Laboratory, University of Chicago | Oct 11, 2016 | - - |
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jan 29, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at