chrX-23722697-T-C
Position:
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2
The NM_001037171.2(ACOT9):āc.457A>Gā(p.Ile153Val) variant causes a missense change. The variant allele was found at a frequency of 0.0000725 in 1,199,758 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 27 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Genomes: š 0.00023 ( 0 hom., 10 hem., cov: 22)
Exomes š: 0.000056 ( 0 hom. 17 hem. )
Consequence
ACOT9
NM_001037171.2 missense
NM_001037171.2 missense
Scores
1
3
11
Clinical Significance
Conservation
PhyloP100: 6.79
Genes affected
ACOT9 (HGNC:17152): (acyl-CoA thioesterase 9) The protein encoded by this gene is a mitochondrial acyl-CoA thioesterase of unknown function. Two transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Mar 2010]
Genome browser will be placed here
ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -6 ACMG points.
BP4
Computational evidence support a benign effect (MetaRNN=0.10797089).
BS2
High Hemizygotes in GnomAd4 at 10 gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ACOT9 | NM_001037171.2 | c.457A>G | p.Ile153Val | missense_variant | 7/16 | ENST00000379303.10 | |
ACOT9 | NM_001033583.3 | c.430A>G | p.Ile144Val | missense_variant | 6/15 | ||
ACOT9 | NM_001330259.2 | c.250A>G | p.Ile84Val | missense_variant | 5/14 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ACOT9 | ENST00000379303.10 | c.457A>G | p.Ile153Val | missense_variant | 7/16 | 1 | NM_001037171.2 | A2 |
Frequencies
GnomAD3 genomes AF: 0.000242 AC: 27AN: 111598Hom.: 0 Cov.: 22 AF XY: 0.000296 AC XY: 10AN XY: 33826
GnomAD3 genomes
AF:
AC:
27
AN:
111598
Hom.:
Cov.:
22
AF XY:
AC XY:
10
AN XY:
33826
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
GnomAD3 exomes AF: 0.000113 AC: 20AN: 177759Hom.: 0 AF XY: 0.0000320 AC XY: 2AN XY: 62417
GnomAD3 exomes
AF:
AC:
20
AN:
177759
Hom.:
AF XY:
AC XY:
2
AN XY:
62417
Gnomad AFR exome
AF:
Gnomad AMR exome
AF:
Gnomad ASJ exome
AF:
Gnomad EAS exome
AF:
Gnomad SAS exome
AF:
Gnomad FIN exome
AF:
Gnomad NFE exome
AF:
Gnomad OTH exome
AF:
GnomAD4 exome AF: 0.0000561 AC: 61AN: 1088108Hom.: 0 Cov.: 27 AF XY: 0.0000479 AC XY: 17AN XY: 354992
GnomAD4 exome
AF:
AC:
61
AN:
1088108
Hom.:
Cov.:
27
AF XY:
AC XY:
17
AN XY:
354992
Gnomad4 AFR exome
AF:
Gnomad4 AMR exome
AF:
Gnomad4 ASJ exome
AF:
Gnomad4 EAS exome
AF:
Gnomad4 SAS exome
AF:
Gnomad4 FIN exome
AF:
Gnomad4 NFE exome
AF:
Gnomad4 OTH exome
AF:
GnomAD4 genome AF: 0.000233 AC: 26AN: 111650Hom.: 0 Cov.: 22 AF XY: 0.000295 AC XY: 10AN XY: 33888
GnomAD4 genome
AF:
AC:
26
AN:
111650
Hom.:
Cov.:
22
AF XY:
AC XY:
10
AN XY:
33888
Gnomad4 AFR
AF:
Gnomad4 AMR
AF:
Gnomad4 ASJ
AF:
Gnomad4 EAS
AF:
Gnomad4 SAS
AF:
Gnomad4 FIN
AF:
Gnomad4 NFE
AF:
Gnomad4 OTH
AF:
Alfa
AF:
Hom.:
Bravo
AF:
ExAC
AF:
AC:
2
ClinVar
Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 02, 2021 | The c.457A>G (p.I153V) alteration is located in exon 7 (coding exon 7) of the ACOT9 gene. This alteration results from a A to G substitution at nucleotide position 457, causing the isoleucine (I) at amino acid position 153 to be replaced by a valine (V). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
CADD
Uncertain
DANN
Uncertain
FATHMM_MKL
Pathogenic
D
LIST_S2
Uncertain
D;D;D;D
M_CAP
Benign
T
MetaRNN
Benign
T;T;T;T
MetaSVM
Benign
T
MutationTaster
Benign
D;D;D;D
PrimateAI
Uncertain
T
PROVEAN
Benign
N;N;N;N
REVEL
Benign
Sift
Benign
T;T;T;T
Sift4G
Benign
T;T;T;T
Polyphen
P;P;.;.
Vest4
MVP
MPC
ClinPred
T
GERP RS
Varity_R
gMVP
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at