chr7-15365594-G-C
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_StrongBP6_Moderate
The NM_001004320.2(AGMO):c.1183C>G(p.Leu395Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000446 in 1,612,550 control chromosomes in the GnomAD database, including 2 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Consequence
NM_001004320.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
AGMO | NM_001004320.2 | c.1183C>G | p.Leu395Val | missense_variant | 12/13 | ENST00000342526.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
AGMO | ENST00000342526.8 | c.1183C>G | p.Leu395Val | missense_variant | 12/13 | 1 | NM_001004320.2 | P1 | |
AGMO | ENST00000407277.6 | c.76C>G | p.Leu26Val | missense_variant | 2/3 | 3 | |||
AGMO | ENST00000418075.1 | c.109C>G | p.Leu37Val | missense_variant | 2/3 | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.00197 AC: 299AN: 151854Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.000698 AC: 175AN: 250754Hom.: 1 AF XY: 0.000502 AC XY: 68AN XY: 135488
GnomAD4 exome AF: 0.000288 AC: 420AN: 1460578Hom.: 2 Cov.: 30 AF XY: 0.000228 AC XY: 166AN XY: 726574
GnomAD4 genome ? AF: 0.00197 AC: 300AN: 151972Hom.: 0 Cov.: 31 AF XY: 0.00214 AC XY: 159AN XY: 74292
ClinVar
Submissions by phenotype
AGMO-related disorder Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | May 03, 2019 | This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at