12-120725939-C-A
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6_Moderate
The NM_000017.4(ACADS):c.46+8C>A variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000132 in 151,758 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_000017.4 splice_region, intron
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ACADS | NM_000017.4 | c.46+8C>A | splice_region_variant, intron_variant | ENST00000242592.9 | |||
ACADS | NM_001302554.2 | c.46+8C>A | splice_region_variant, intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ACADS | ENST00000242592.9 | c.46+8C>A | splice_region_variant, intron_variant | 1 | NM_000017.4 | P1 | |||
ACADS | ENST00000411593.2 | c.46+8C>A | splice_region_variant, intron_variant | 2 | |||||
ACADS | ENST00000539690.1 | n.158+8C>A | splice_region_variant, intron_variant, non_coding_transcript_variant | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.0000132 AC: 2AN: 151758Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.00000706 AC: 1AN: 141554Hom.: 0 AF XY: 0.0000126 AC XY: 1AN XY: 79078
GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0AN: 1391500Hom.: 0 Cov.: 31 AF XY: 0.00 AC XY: 0AN XY: 688936
GnomAD4 genome ? AF: 0.0000132 AC: 2AN: 151758Hom.: 0 Cov.: 31 AF XY: 0.0000135 AC XY: 1AN XY: 74118
ClinVar
Submissions by phenotype
Deficiency of butyryl-CoA dehydrogenase Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Nov 16, 2020 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at