chr12-81134865-A-T
Variant summary
Our verdict is Likely pathogenic. Variant got 6 ACMG points: 6P and 0B. PM2PP3_Strong
The NM_024560.4(ACSS3):c.506A>T(p.Asp169Val) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00000138 in 1,444,460 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic 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_pathogenic. Variant got 6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ACSS3 | NM_024560.4 | c.506A>T | p.Asp169Val | missense_variant | 3/16 | ENST00000548058.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ACSS3 | ENST00000548058.6 | c.506A>T | p.Asp169Val | missense_variant | 3/16 | 1 | NM_024560.4 | A1 | |
ACSS3 | ENST00000261206.7 | c.503A>T | p.Asp168Val | missense_variant | 3/16 | 1 | P4 | ||
ACSS3 | ENST00000549175.1 | c.182A>T | p.Asp61Val | missense_variant | 4/4 | 5 | |||
ACSS3 | ENST00000548387.1 | n.71A>T | non_coding_transcript_exon_variant | 1/3 | 2 |
Frequencies
GnomAD3 genomes ? Cov.: 30
GnomAD4 exome AF: 0.00000138 AC: 2AN: 1444460Hom.: 0 Cov.: 30 AF XY: 0.00 AC XY: 0AN XY: 718214
GnomAD4 genome ? Cov.: 30
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jan 05, 2022 | The c.506A>T (p.D169V) alteration is located in exon 3 (coding exon 3) of the ACSS3 gene. This alteration results from a A to T substitution at nucleotide position 506, causing the aspartic acid (D) at amino acid position 169 to be replaced by a valine (V). 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
Publications
No publications associated with this variant yet.