rs2291447
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BA1
The ENST00000591859.5(ACBD4):c.-153+4G>T variant causes a splice donor region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.461 in 154,056 control chromosomes in the GnomAD database, including 16,733 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.46 ( 16499 hom., cov: 34)
Exomes 𝑓: 0.44 ( 234 hom. )
Consequence
ACBD4
ENST00000591859.5 splice_donor_region, intron
ENST00000591859.5 splice_donor_region, intron
Scores
2
Splicing: ADA: 0.9739
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.406
Genes affected
ACBD4 (HGNC:23337): (acyl-CoA binding domain containing 4) This gene encodes a member of the acyl-coenzyme A binding domain containing protein family. All family members contain the conserved acyl-Coenzyme A binding domain, which binds acyl-CoA thiol esters. They are thought to play roles in acyl-CoA dependent lipid metabolism. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Oct 2008]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -8 ACMG points.
BA1
?
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.524 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ACBD4 | NM_001378112.1 | c.-700G>T | 5_prime_UTR_variant | 2/10 | |||
ACBD4 | XM_006722085.3 | c.-395G>T | 5_prime_UTR_variant | 2/11 | |||
ACBD4 | XM_011525259.3 | c.-395G>T | 5_prime_UTR_variant | 2/10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ACBD4 | ENST00000591859.5 | c.-153+4G>T | splice_donor_region_variant, intron_variant | 1 | |||||
ACBD4 | ENST00000431281.5 | c.-150G>T | splice_region_variant, 5_prime_UTR_variant | 2/12 | 5 | ||||
ACBD4 | ENST00000619916.4 | c.-150G>T | splice_region_variant, 5_prime_UTR_variant | 2/12 | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.461 AC: 70099AN: 152038Hom.: 16491 Cov.: 34
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GnomAD4 exome AF: 0.442 AC: 839AN: 1900Hom.: 234 Cov.: 0 AF XY: 0.474 AC XY: 539AN XY: 1138
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GnomAD4 genome ? AF: 0.461 AC: 70130AN: 152156Hom.: 16499 Cov.: 34 AF XY: 0.457 AC XY: 33994AN XY: 74388
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ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
Splicing
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Calibrated prediction
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dbscSNV1_ADA
Pathogenic
dbscSNV1_RF
Pathogenic
Find out detailed SpliceAI scores and Pangolin per-transcript scores at