6-24667308-G-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_018473.4(ACOT13):c.45G>T(p.Met15Ile) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000892 in 1,614,230 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Another nucleotide change resulting in same amino acid change has been previously reported as Uncertain significancein ClinVar.
Frequency
Consequence
NM_018473.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ACOT13 | NM_018473.4 | c.45G>T | p.Met15Ile | missense_variant | 1/3 | ENST00000230048.5 | |
ACOT13 | NM_001160094.2 | c.-314G>T | 5_prime_UTR_variant | 1/4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ACOT13 | ENST00000230048.5 | c.45G>T | p.Met15Ile | missense_variant | 1/3 | 1 | NM_018473.4 | P1 | |
ACOT13 | ENST00000537591.5 | c.-314G>T | 5_prime_UTR_variant | 1/4 | 1 |
Frequencies
GnomAD3 genomes AF: 0.0000657 AC: 10AN: 152248Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000557 AC: 14AN: 251374Hom.: 0 AF XY: 0.0000662 AC XY: 9AN XY: 135884
GnomAD4 exome AF: 0.0000917 AC: 134AN: 1461864Hom.: 0 Cov.: 31 AF XY: 0.0000921 AC XY: 67AN XY: 727234
GnomAD4 genome AF: 0.0000656 AC: 10AN: 152366Hom.: 0 Cov.: 33 AF XY: 0.000107 AC XY: 8AN XY: 74512
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Mar 02, 2023 | The c.45G>T (p.M15I) alteration is located in exon 1 (coding exon 1) of the ACOT13 gene. This alteration results from a G to T substitution at nucleotide position 45, causing the methionine (M) at amino acid position 15 to be replaced by an isoleucine (I). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at