chr12-11650167-A-G
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+7A>G variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000391 in 1,612,566 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 Likely benign (★★).
Frequency
Consequence
NM_001987.5 splice_region, intron
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ETV6 | NM_001987.5 | c.33+7A>G | splice_region_variant, intron_variant | ENST00000396373.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ETV6 | ENST00000396373.9 | c.33+7A>G | splice_region_variant, intron_variant | 1 | NM_001987.5 | P1 | |||
ETV6 | ENST00000541426.1 | n.217+7A>G | splice_region_variant, intron_variant, non_coding_transcript_variant | 4 | |||||
ETV6 | ENST00000544715.1 | n.150+7A>G | splice_region_variant, intron_variant, non_coding_transcript_variant | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.0000658 AC: 10AN: 151982Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.0000160 AC: 4AN: 249642Hom.: 0 AF XY: 0.0000296 AC XY: 4AN XY: 135164
GnomAD4 exome AF: 0.0000363 AC: 53AN: 1460584Hom.: 0 Cov.: 29 AF XY: 0.0000427 AC XY: 31AN XY: 726696
GnomAD4 genome ? AF: 0.0000658 AC: 10AN: 151982Hom.: 0 Cov.: 31 AF XY: 0.000108 AC XY: 8AN XY: 74238
ClinVar
Submissions by phenotype
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Genetic Services Laboratory, University of Chicago | Apr 23, 2019 | - - |
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jan 02, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at