X-112778585-C-T
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2
The NM_001113490.2(AMOT):c.3237G>A(p.Met1079Ile) variant causes a missense change. The variant allele was found at a frequency of 0.0000166 in 1,203,984 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 4 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001113490.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
AMOT | ENST00000371959.9 | c.3237G>A | p.Met1079Ile | missense_variant | Exon 14 of 14 | 1 | NM_001113490.2 | ENSP00000361027.3 | ||
AMOT | ENST00000371962.5 | c.2541G>A | p.Met847Ile | missense_variant | Exon 11 of 11 | 1 | ENSP00000361030.1 | |||
AMOT | ENST00000304758.5 | c.2010G>A | p.Met670Ile | missense_variant | Exon 12 of 12 | 1 | ENSP00000305557.1 |
Frequencies
GnomAD3 genomes AF: 0.00000890 AC: 1AN: 112363Hom.: 0 Cov.: 24 AF XY: 0.00 AC XY: 0AN XY: 34523
GnomAD3 exomes AF: 0.0000110 AC: 2AN: 181661Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 66185
GnomAD4 exome AF: 0.0000174 AC: 19AN: 1091621Hom.: 0 Cov.: 28 AF XY: 0.0000112 AC XY: 4AN XY: 357561
GnomAD4 genome AF: 0.00000890 AC: 1AN: 112363Hom.: 0 Cov.: 24 AF XY: 0.00 AC XY: 0AN XY: 34523
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.3237G>A (p.M1079I) alteration is located in exon 11 (coding exon 11) of the AMOT gene. This alteration results from a G to A substitution at nucleotide position 3237, causing the methionine (M) at amino acid position 1079 to be replaced by an isoleucine (I). 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