3-184242661-C-T
Variant summary
Our verdict is Likely benign. Variant got -3 ACMG points: 2P and 5B. PM2BP4_StrongBP7
The NM_005787.6(ALG3):c.1170G>A(p.Gly390Gly) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000103 in 1,560,610 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Synonymous variant affecting the same amino acid position (i.e. G390G) has been classified as Likely benign.
Frequency
Consequence
NM_005787.6 synonymous
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 rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
ALG3 | NM_005787.6 | c.1170G>A | p.Gly390Gly | synonymous_variant | Exon 9 of 9 | ENST00000397676.8 | NP_005778.1 | |
ALG3 | NM_001006941.2 | c.1026G>A | p.Gly342Gly | synonymous_variant | Exon 9 of 9 | NP_001006942.1 | ||
ALG3 | NR_024533.1 | n.1101G>A | non_coding_transcript_exon_variant | Exon 8 of 8 | ||||
ALG3 | NR_024534.1 | n.1164G>A | non_coding_transcript_exon_variant | Exon 9 of 9 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152230Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000144 AC: 3AN: 208820Hom.: 0 AF XY: 0.0000180 AC XY: 2AN XY: 111018
GnomAD4 exome AF: 0.0000107 AC: 15AN: 1408380Hom.: 0 Cov.: 32 AF XY: 0.0000101 AC XY: 7AN XY: 693034
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152230Hom.: 0 Cov.: 33 AF XY: 0.00 AC XY: 0AN XY: 74376
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at