rs78348923
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The NM_000642.3(AGL):āc.4430C>Gā(p.Thr1477Ser) variant causes a missense change. The variant allele was found at a frequency of 0.000865 in 1,613,216 control chromosomes in the GnomAD database, including 6 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (ā ā ). Synonymous variant affecting the same amino acid position (i.e. T1477T) has been classified as Likely benign.
Frequency
Consequence
NM_000642.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
AGL | NM_000642.3 | c.4430C>G | p.Thr1477Ser | missense_variant | 33/34 | ENST00000361915.8 | |
LOC124904230 | XR_007066249.1 | n.1146-3463G>C | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
AGL | ENST00000361915.8 | c.4430C>G | p.Thr1477Ser | missense_variant | 33/34 | 1 | NM_000642.3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00493 AC: 749AN: 152018Hom.: 4 Cov.: 32
GnomAD3 exomes AF: 0.00120 AC: 301AN: 250836Hom.: 1 AF XY: 0.000885 AC XY: 120AN XY: 135580
GnomAD4 exome AF: 0.000441 AC: 645AN: 1461080Hom.: 2 Cov.: 31 AF XY: 0.000369 AC XY: 268AN XY: 726840
GnomAD4 genome ? AF: 0.00494 AC: 751AN: 152136Hom.: 4 Cov.: 32 AF XY: 0.00484 AC XY: 360AN XY: 74370
ClinVar
Submissions by phenotype
Glycogen storage disease type III Benign:3
Benign, criteria provided, single submitter | clinical testing | Genome-Nilou Lab | Jul 15, 2021 | - - |
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 31, 2024 | - - |
Likely benign, criteria provided, single submitter | clinical testing | Fulgent Genetics, Fulgent Genetics | Jul 23, 2021 | - - |
not provided Benign:2
Likely benign, criteria provided, single submitter | clinical testing | Center for Pediatric Genomic Medicine, Children's Mercy Hospital and Clinics | Jan 23, 2017 | - - |
Benign, criteria provided, single submitter | clinical testing | GeneDx | Nov 14, 2019 | - - |
AGL-related disorder Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Sep 17, 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