10-123034358-A-C
Variant summary
Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_StrongBP6_ModerateBP7BS2
The NM_001609.4(ACADSB):c.45A>C(p.Leu15=) variant causes a splice region, synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000173 in 1,613,654 control chromosomes in the GnomAD database, including 3 homozygotes. In-silico tool predicts a benign outcome for this variant. 1/1 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Benign (★).
Frequency
Consequence
NM_001609.4 splice_region, synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -11 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ACADSB | NM_001609.4 | c.45A>C | p.Leu15= | splice_region_variant, synonymous_variant | 2/11 | ENST00000358776.7 | |
ACADSB | NM_001330174.3 | c.-161A>C | splice_region_variant, 5_prime_UTR_variant | 2/10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ACADSB | ENST00000358776.7 | c.45A>C | p.Leu15= | splice_region_variant, synonymous_variant | 2/11 | 1 | NM_001609.4 | P1 | |
ACADSB | ENST00000368869.8 | c.-161A>C | splice_region_variant, 5_prime_UTR_variant | 2/10 | 2 | ||||
ACADSB | ENST00000411816.2 | n.62A>C | splice_region_variant, non_coding_transcript_exon_variant | 2/4 | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.0000788 AC: 12AN: 152222Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000378 AC: 95AN: 251126Hom.: 3 AF XY: 0.000567 AC XY: 77AN XY: 135802
GnomAD4 exome AF: 0.000183 AC: 267AN: 1461314Hom.: 3 Cov.: 31 AF XY: 0.000286 AC XY: 208AN XY: 727006
GnomAD4 genome ? AF: 0.0000788 AC: 12AN: 152340Hom.: 0 Cov.: 32 AF XY: 0.000121 AC XY: 9AN XY: 74504
ClinVar
Submissions by phenotype
Deficiency of 2-methylbutyryl-CoA dehydrogenase Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Apr 29, 2021 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at