16-20623511-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001318890.3(ACSM1):c.1709G>A(p.Arg570Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000843 in 1,613,970 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001318890.3 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 |
---|---|---|---|---|---|---|---|
ACSM1 | NM_001318890.3 | c.1709G>A | p.Arg570Gln | missense_variant | 14/14 | ENST00000520010.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ACSM1 | ENST00000520010.6 | c.1709G>A | p.Arg570Gln | missense_variant | 14/14 | 1 | NM_001318890.3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.000164 AC: 25AN: 152160Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000147 AC: 37AN: 251448Hom.: 0 AF XY: 0.000184 AC XY: 25AN XY: 135894
GnomAD4 exome AF: 0.0000759 AC: 111AN: 1461810Hom.: 0 Cov.: 31 AF XY: 0.0000756 AC XY: 55AN XY: 727210
GnomAD4 genome ? AF: 0.000164 AC: 25AN: 152160Hom.: 0 Cov.: 33 AF XY: 0.000188 AC XY: 14AN XY: 74324
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Apr 24, 2023 | The c.1709G>A (p.R570Q) alteration is located in exon 13 (coding exon 13) of the ACSM1 gene. This alteration results from a G to A substitution at nucleotide position 1709, causing the arginine (R) at amino acid position 570 to be replaced by a glutamine (Q). 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