rs10561331

Variant summary

Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2

The NM_001386681.1(ACAT1):​c.-199+4310_-199+4315delAAAAAA variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000397 in 252,142 control chromosomes in the GnomAD database, with no homozygous occurrence. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.000014 ( 0 hom., cov: 0)
Exomes 𝑓: 0.000073 ( 0 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]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 2 ACMG points.

PM2
Very rare variant in population databases, with high coverage;

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
ACAT1NM_001386681.1 linkc.-199+4310_-199+4315delAAAAAA intron_variant Intron 1 of 11 NP_001373610.1
ACAT1NM_001386682.1 linkc.-416+4310_-416+4315delAAAAAA 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+4304delAAAAAA intron_variant Intron 1 of 11 ENSP00000500444.1 A0A5F9ZHJ0
ENSG00000255467ENST00000525548.1 linkn.389+90_389+95delTTTTTT intron_variant Intron 1 of 3 3

Frequencies

GnomAD3 genomes
AF:
0.0000141
AC:
2
AN:
142076
Hom.:
0
Cov.:
0
show subpopulations
Gnomad AFR
AF:
0.00
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.000140
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.00
Gnomad OTH
AF:
0.00
GnomAD4 exome
AF:
0.0000727
AC:
8
AN:
109998
Hom.:
0
AF XY:
0.0000679
AC XY:
4
AN XY:
58930
show subpopulations
Gnomad4 AFR exome
AF:
0.00
Gnomad4 AMR exome
AF:
0.00
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.000264
Gnomad4 SAS exome
AF:
0.000192
Gnomad4 FIN exome
AF:
0.000157
Gnomad4 NFE exome
AF:
0.0000311
Gnomad4 OTH exome
AF:
0.00
GnomAD4 genome
AF:
0.0000141
AC:
2
AN:
142144
Hom.:
0
Cov.:
0
AF XY:
0.00
AC XY:
0
AN XY:
68714
show subpopulations
Gnomad4 AFR
AF:
0.00
Gnomad4 AMR
AF:
0.000140
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.00
Gnomad4 OTH
AF:
0.00

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