6-159762928-A-G
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_005891.3(ACAT2):āc.65A>Gā(p.Asn22Ser) variant causes a missense change. The variant allele was found at a frequency of 0.0001 in 1,612,304 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. 12/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. N22T) has been classified as Uncertain significance.
Frequency
Consequence
NM_005891.3 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ACAT2 | NM_005891.3 | c.65A>G | p.Asn22Ser | missense_variant | 2/9 | ENST00000367048.5 | |
ACAT2 | NM_001303253.1 | c.152A>G | p.Asn51Ser | missense_variant | 2/9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ACAT2 | ENST00000367048.5 | c.65A>G | p.Asn22Ser | missense_variant | 2/9 | 1 | NM_005891.3 | P1 | |
ACAT2 | ENST00000467951.1 | n.293A>G | non_coding_transcript_exon_variant | 2/5 | 3 |
Frequencies
GnomAD3 genomes AF: 0.000276 AC: 42AN: 152140Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000132 AC: 33AN: 249328Hom.: 0 AF XY: 0.000126 AC XY: 17AN XY: 134860
GnomAD4 exome AF: 0.0000822 AC: 120AN: 1460046Hom.: 1 Cov.: 32 AF XY: 0.0000909 AC XY: 66AN XY: 726392
GnomAD4 genome AF: 0.000276 AC: 42AN: 152258Hom.: 0 Cov.: 32 AF XY: 0.000363 AC XY: 27AN XY: 74454
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 20, 2023 | The c.65A>G (p.N22S) alteration is located in exon 2 (coding exon 2) of the ACAT2 gene. This alteration results from a A to G substitution at nucleotide position 65, causing the asparagine (N) at amino acid position 22 to be replaced by a serine (S). 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