chr12-81143111-C-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_024560.4(ACSS3):c.785C>A(p.Ala262Glu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000242 in 1,611,370 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 (★).
Frequency
Consequence
NM_024560.4 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 |
---|---|---|---|---|---|---|---|
ACSS3 | NM_024560.4 | c.785C>A | p.Ala262Glu | missense_variant | 5/16 | ENST00000548058.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ACSS3 | ENST00000548058.6 | c.785C>A | p.Ala262Glu | missense_variant | 5/16 | 1 | NM_024560.4 | A1 | |
ACSS3 | ENST00000261206.7 | c.782C>A | p.Ala261Glu | missense_variant | 5/16 | 1 | P4 | ||
ACSS3 | ENST00000548387.1 | n.350C>A | non_coding_transcript_exon_variant | 3/3 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.0000526 AC: 8AN: 152132Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000719 AC: 18AN: 250452Hom.: 0 AF XY: 0.0000591 AC XY: 8AN XY: 135384
GnomAD4 exome AF: 0.0000212 AC: 31AN: 1459120Hom.: 0 Cov.: 30 AF XY: 0.0000248 AC XY: 18AN XY: 725890
GnomAD4 genome ? AF: 0.0000525 AC: 8AN: 152250Hom.: 0 Cov.: 33 AF XY: 0.0000672 AC XY: 5AN XY: 74452
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jul 12, 2023 | The c.785C>A (p.A262E) alteration is located in exon 5 (coding exon 5) of the ACSS3 gene. This alteration results from a C to A substitution at nucleotide position 785, causing the alanine (A) at amino acid position 262 to be replaced by a glutamic acid (E). 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