chr6-159768558-G-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_005891.3(ACAT2):c.420G>A(p.Met140Ile) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000558 in 1,614,050 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. M140K) has been classified as Uncertain significance.
Frequency
Consequence
NM_005891.3 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 |
---|---|---|---|---|---|---|---|
ACAT2 | NM_005891.3 | c.420G>A | p.Met140Ile | missense_variant | 4/9 | ENST00000367048.5 | |
ACAT2 | NM_001303253.1 | c.507G>A | p.Met169Ile | missense_variant | 4/9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ACAT2 | ENST00000367048.5 | c.420G>A | p.Met140Ile | missense_variant | 4/9 | 1 | NM_005891.3 | P1 | |
ACAT2 | ENST00000467951.1 | n.648G>A | non_coding_transcript_exon_variant | 4/5 | 3 |
Frequencies
GnomAD3 genomes AF: 0.0000328 AC: 5AN: 152208Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000119 AC: 3AN: 251418Hom.: 0 AF XY: 0.0000147 AC XY: 2AN XY: 135884
GnomAD4 exome AF: 0.00000137 AC: 2AN: 1461724Hom.: 0 Cov.: 30 AF XY: 0.00000138 AC XY: 1AN XY: 727170
GnomAD4 genome AF: 0.0000460 AC: 7AN: 152326Hom.: 0 Cov.: 33 AF XY: 0.0000806 AC XY: 6AN XY: 74476
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at