16-20483086-C-T
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_001308172.2(ACSM2A):c.1538C>T(p.Ser513Leu) variant causes a missense change. The variant allele was found at a frequency of 0.11 in 1,613,714 control chromosomes in the GnomAD database, including 10,859 homozygotes. In-silico tool predicts a benign outcome for this variant. 12/20 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another nucleotide change resulting in the same amino acid substitution has been previously reported as Likely benign in UniProt.
Frequency
Consequence
NM_001308172.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -12 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.117 AC: 17768AN: 151990Hom.: 1175 Cov.: 31
GnomAD3 exomes AF: 0.128 AC: 32100AN: 251472Hom.: 2395 AF XY: 0.130 AC XY: 17699AN XY: 135910
GnomAD4 exome AF: 0.109 AC: 159410AN: 1461606Hom.: 9681 Cov.: 31 AF XY: 0.112 AC XY: 81179AN XY: 727086
GnomAD4 genome AF: 0.117 AC: 17786AN: 152108Hom.: 1178 Cov.: 31 AF XY: 0.121 AC XY: 8992AN XY: 74344
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at