rs2307130
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_000642.3(AGL):c.-10A>G variant causes a 5 prime UTR premature start codon gain change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.484 in 1,610,628 control chromosomes in the GnomAD database, including 191,964 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Consequence
NM_000642.3 5_prime_UTR_premature_start_codon_gain
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 rank | MANE | Protein | UniProt |
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AGL | NM_000642.3 | c.-10A>G | 5_prime_UTR_premature_start_codon_gain_variant | Exon 2 of 34 | ENST00000361915.8 | NP_000633.2 | ||
AGL | NM_000642.3 | c.-10A>G | 5_prime_UTR_variant | Exon 2 of 34 | ENST00000361915.8 | NP_000633.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
AGL | ENST00000361915 | c.-10A>G | 5_prime_UTR_premature_start_codon_gain_variant | Exon 2 of 34 | 1 | NM_000642.3 | ENSP00000355106.3 | |||
AGL | ENST00000361915 | c.-10A>G | 5_prime_UTR_variant | Exon 2 of 34 | 1 | NM_000642.3 | ENSP00000355106.3 |
Frequencies
GnomAD3 genomes AF: 0.419 AC: 63647AN: 151976Hom.: 14073 Cov.: 33
GnomAD3 exomes AF: 0.469 AC: 117972AN: 251340Hom.: 28421 AF XY: 0.479 AC XY: 65025AN XY: 135874
GnomAD4 exome AF: 0.491 AC: 715475AN: 1458534Hom.: 177867 Cov.: 31 AF XY: 0.493 AC XY: 357476AN XY: 725786
GnomAD4 genome AF: 0.419 AC: 63701AN: 152094Hom.: 14097 Cov.: 33 AF XY: 0.420 AC XY: 31205AN XY: 74338
ClinVar
Submissions by phenotype
Glycogen storage disease type III Benign:4
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This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease. -
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not specified Benign:3
This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. -
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not provided Benign:2
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at