X-112780981-T-C
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2
The NM_001113490.2(AMOT):āc.2378A>Gā(p.Asn793Ser) variant causes a missense change. The variant allele was found at a frequency of 0.000112 in 1,210,330 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 41 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ).
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.2378A>G | p.Asn793Ser | missense_variant | Exon 12 of 14 | 1 | NM_001113490.2 | ENSP00000361027.3 | ||
AMOT | ENST00000371962.5 | c.1682A>G | p.Asn561Ser | missense_variant | Exon 9 of 11 | 1 | ENSP00000361030.1 | |||
AMOT | ENST00000304758.5 | c.1151A>G | p.Asn384Ser | missense_variant | Exon 10 of 12 | 1 | ENSP00000305557.1 | |||
AMOT | ENST00000371958.1 | c.1682A>G | p.Asn561Ser | missense_variant | Exon 9 of 9 | 5 | ENSP00000361026.1 |
Frequencies
GnomAD3 genomes AF: 0.0000625 AC: 7AN: 112062Hom.: 0 Cov.: 22 AF XY: 0.0000292 AC XY: 1AN XY: 34232
GnomAD3 exomes AF: 0.0000491 AC: 9AN: 183418Hom.: 0 AF XY: 0.0000737 AC XY: 5AN XY: 67850
GnomAD4 exome AF: 0.000117 AC: 129AN: 1098216Hom.: 0 Cov.: 30 AF XY: 0.000110 AC XY: 40AN XY: 363572
GnomAD4 genome AF: 0.0000624 AC: 7AN: 112114Hom.: 0 Cov.: 22 AF XY: 0.0000292 AC XY: 1AN XY: 34294
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.2378A>G (p.N793S) alteration is located in exon 9 (coding exon 9) of the AMOT gene. This alteration results from a A to G substitution at nucleotide position 2378, causing the asparagine (N) at amino acid position 793 to be replaced by a serine (S). 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