chr1-99876507-A-G
Variant summary
Our verdict is Likely benign. Variant got -3 ACMG points: 2P and 5B. PM2BP4_StrongBP6
The NM_000642.3(AGL):āc.1333A>Gā(p.Met445Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000478 in 1,611,624 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 16/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Consequence
NM_000642.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -3 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
AGL | NM_000642.3 | c.1333A>G | p.Met445Val | missense_variant | 11/34 | ENST00000361915.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
AGL | ENST00000361915.8 | c.1333A>G | p.Met445Val | missense_variant | 11/34 | 1 | NM_000642.3 | P1 |
Frequencies
GnomAD3 genomes AF: 0.000269 AC: 41AN: 152228Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000717 AC: 18AN: 251096Hom.: 0 AF XY: 0.0000663 AC XY: 9AN XY: 135700
GnomAD4 exome AF: 0.0000247 AC: 36AN: 1459396Hom.: 0 Cov.: 30 AF XY: 0.0000220 AC XY: 16AN XY: 726144
GnomAD4 genome AF: 0.000269 AC: 41AN: 152228Hom.: 0 Cov.: 33 AF XY: 0.000269 AC XY: 20AN XY: 74374
ClinVar
Submissions by phenotype
Glycogen storage disease type III Uncertain:1Benign:1
Uncertain significance, no assertion criteria provided | clinical testing | Natera, Inc. | Oct 28, 2019 | - - |
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jan 19, 2024 | - - |
not provided Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Mayo Clinic Laboratories, Mayo Clinic | May 23, 2023 | BP4 - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at