chr12-53307533-C-T
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The NM_015665.6(AAAS):c.1597G>A(p.Gly533Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00146 in 1,614,100 control chromosomes in the GnomAD database, including 37 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Consequence
NM_015665.6 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
AAAS | NM_015665.6 | c.1597G>A | p.Gly533Arg | missense_variant | 16/16 | ENST00000209873.9 | NP_056480.1 | |
AAAS | NM_001173466.2 | c.1498G>A | p.Gly500Arg | missense_variant | 15/15 | NP_001166937.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
AAAS | ENST00000209873.9 | c.1597G>A | p.Gly533Arg | missense_variant | 16/16 | 1 | NM_015665.6 | ENSP00000209873.4 |
Frequencies
GnomAD3 genomes AF: 0.00784 AC: 1193AN: 152166Hom.: 20 Cov.: 33
GnomAD3 exomes AF: 0.00194 AC: 485AN: 250548Hom.: 6 AF XY: 0.00149 AC XY: 202AN XY: 135522
GnomAD4 exome AF: 0.000793 AC: 1159AN: 1461816Hom.: 17 Cov.: 34 AF XY: 0.000668 AC XY: 486AN XY: 727198
GnomAD4 genome AF: 0.00787 AC: 1198AN: 152284Hom.: 20 Cov.: 33 AF XY: 0.00753 AC XY: 561AN XY: 74476
ClinVar
Submissions by phenotype
not provided Benign:2
Likely benign, criteria provided, single submitter | not provided | Breakthrough Genomics, Breakthrough Genomics | - | - - |
Benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Jan 31, 2024 | - - |
Glucocorticoid deficiency with achalasia Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Jun 14, 2016 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at