chr7-15366196-CAGA-C
Variant summary
Our verdict is Uncertain significance. Variant got 3 ACMG points: 3P and 0B. PM2PM4_Supporting
The NM_001004320.2(AGMO):c.1098_1100delTCT(p.Leu367del) variant causes a disruptive inframe deletion change. The variant allele was found at a frequency of 0.0000367 in 1,608,256 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001004320.2 disruptive_inframe_deletion
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Uncertain_significance. Variant got 3 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
AGMO | ENST00000342526.8 | c.1098_1100delTCT | p.Leu367del | disruptive_inframe_deletion | Exon 11 of 13 | 1 | NM_001004320.2 | ENSP00000341662.3 | ||
AGMO | ENST00000418075.1 | c.24_26delTCT | p.Leu9del | disruptive_inframe_deletion | Exon 1 of 3 | 3 | ENSP00000394412.1 | |||
AGMO | ENST00000407277.6 | c.-13_-11delTCT | upstream_gene_variant | 3 | ENSP00000385742.2 |
Frequencies
GnomAD3 genomes AF: 0.0000921 AC: 14AN: 152060Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000698 AC: 17AN: 243642Hom.: 0 AF XY: 0.0000228 AC XY: 3AN XY: 131720
GnomAD4 exome AF: 0.0000309 AC: 45AN: 1456080Hom.: 0 AF XY: 0.00000967 AC XY: 7AN XY: 724066
GnomAD4 genome AF: 0.0000920 AC: 14AN: 152176Hom.: 0 Cov.: 33 AF XY: 0.0000941 AC XY: 7AN XY: 74400
ClinVar
Submissions by phenotype
AGMO-related Neurodevelopmental disorder Uncertain:1
The inherited heterozygous c.1098_1100del, p.Leu367del inframe deletion identified in the AGMO gene has not been reported in affected individuals in the literature or in the ClinVar database. The variant has 0.00009207 allele frequency in the gnomAD(v3) database (14 out of 152060 heterozygous alleles, no homozygotes) suggesting it is not a common benign variant in the populations represented in that database. The variant affects a moderately conserved amino acid. Based on the available evidence, the inherited heterozygous c.1098_1100del, p.Leu367del variant identified in the AGMO gene is reported as a Variant of Uncertain Significance. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at