11-108121200-CAAAAAA-CAAA

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BA1

The NM_001386681.1(ACAT1):​c.-199+4313_-199+4315delAAA variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0921 in 249,200 control chromosomes in the GnomAD database, including 21 homozygotes. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.010 ( 19 hom., cov: 0)
Exomes 𝑓: 0.20 ( 2 hom. )

Consequence

ACAT1
NM_001386681.1 intron

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.702
Variant links:
Genes affected
ACAT1 (HGNC:93): (acetyl-CoA acetyltransferase 1) This gene encodes a mitochondrially localized enzyme that catalyzes the reversible formation of acetoacetyl-CoA from two molecules of acetyl-CoA. Defects in this gene are associated with 3-ketothiolase deficiency, an inborn error of isoleucine catabolism characterized by urinary excretion of 2-methyl-3-hydroxybutyric acid, 2-methylacetoacetic acid, tiglylglycine, and butanone. [provided by RefSeq, Feb 2009]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -8 ACMG points.

BA1
GnomAdExome4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.302 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
ACAT1NM_001386681.1 linkc.-199+4313_-199+4315delAAA intron_variant Intron 1 of 11 NP_001373610.1
ACAT1NM_001386682.1 linkc.-416+4313_-416+4315delAAA intron_variant Intron 1 of 12 NP_001373611.1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
ACAT1ENST00000672284.1 linkc.-199+4299_-199+4301delAAA intron_variant Intron 1 of 11 ENSP00000500444.1 A0A5F9ZHJ0
ENSG00000255467ENST00000525548.1 linkn.389+93_389+95delTTT intron_variant Intron 1 of 3 3

Frequencies

GnomAD3 genomes
AF:
0.0102
AC:
1446
AN:
141968
Hom.:
19
Cov.:
0
show subpopulations
Gnomad AFR
AF:
0.0287
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00617
Gnomad ASJ
AF:
0.00240
Gnomad EAS
AF:
0.00103
Gnomad SAS
AF:
0.000885
Gnomad FIN
AF:
0.00864
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.00212
Gnomad OTH
AF:
0.0104
GnomAD4 exome
AF:
0.201
AC:
21494
AN:
107166
Hom.:
2
AF XY:
0.203
AC XY:
11649
AN XY:
57374
show subpopulations
Gnomad4 AFR exome
AF:
0.219
Gnomad4 AMR exome
AF:
0.221
Gnomad4 ASJ exome
AF:
0.185
Gnomad4 EAS exome
AF:
0.317
Gnomad4 SAS exome
AF:
0.234
Gnomad4 FIN exome
AF:
0.177
Gnomad4 NFE exome
AF:
0.184
Gnomad4 OTH exome
AF:
0.192
GnomAD4 genome
AF:
0.0102
AC:
1453
AN:
142034
Hom.:
19
Cov.:
0
AF XY:
0.0104
AC XY:
717
AN XY:
68656
show subpopulations
Gnomad4 AFR
AF:
0.0288
Gnomad4 AMR
AF:
0.00616
Gnomad4 ASJ
AF:
0.00240
Gnomad4 EAS
AF:
0.00104
Gnomad4 SAS
AF:
0.000888
Gnomad4 FIN
AF:
0.00864
Gnomad4 NFE
AF:
0.00212
Gnomad4 OTH
AF:
0.0114

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs10561331; hg19: chr11-107991927; API