15-45362081-G-A
Variant summary
Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBS1BS2
The ENST00000558362.5(GATM):n.2956C>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000633 in 1,391,220 control chromosomes in the GnomAD database, including 7 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Consequence
ENST00000558362.5 non_coding_transcript_exon
Scores
Clinical Significance
Conservation
Publications
- AGAT deficiencyInheritance: AR Classification: DEFINITIVE, STRONG, MODERATE, SUPPORTIVE Submitted by: Labcorp Genetics (formerly Invitae), ClinGen, Orphanet, Ambry Genetics, G2P
- Fanconi renotubular syndrome 1Inheritance: AD Classification: MODERATE Submitted by: Ambry Genetics
- primary Fanconi syndromeInheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet
Genome browser will be placed here
ACMG classification
Our verdict: Benign. The variant received -12 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
GATM | NM_001482.3 | c.*28C>T | 3_prime_UTR_variant | Exon 9 of 9 | ENST00000396659.8 | NP_001473.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.000335 AC: 51AN: 152152Hom.: 0 Cov.: 32 show subpopulations
GnomAD2 exomes AF: 0.00125 AC: 314AN: 250458 AF XY: 0.00173 show subpopulations
GnomAD4 exome AF: 0.000668 AC: 828AN: 1238950Hom.: 7 Cov.: 18 AF XY: 0.000971 AC XY: 609AN XY: 627406 show subpopulations
GnomAD4 genome AF: 0.000341 AC: 52AN: 152270Hom.: 0 Cov.: 32 AF XY: 0.000551 AC XY: 41AN XY: 74470 show subpopulations
ClinVar
Submissions by phenotype
Arginine:glycine amidinotransferase deficiency Benign:1
This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as likely benign is not then subjected to further curation. The score for this variant resulted in a classification of likely benign for this disease. -
not provided Benign:1
- -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at