chr16-5071858-C-T
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 2P and 7B. PM2BP4_StrongBP6_ModerateBP7
The NM_019109.5(ALG1):c.9C>T(p.Ala3Ala) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000436 in 1,604,784 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★). Synonymous variant affecting the same amino acid position (i.e. A3A) has been classified as Likely benign.
Frequency
Consequence
NM_019109.5 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -5 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
ALG1 | NM_019109.5 | c.9C>T | p.Ala3Ala | synonymous_variant | Exon 1 of 13 | ENST00000262374.10 | NP_061982.3 | |
ALG1 | XM_017023457.3 | c.9C>T | p.Ala3Ala | synonymous_variant | Exon 1 of 12 | XP_016878946.1 | ||
ALG1 | XR_007064892.1 | n.16C>T | non_coding_transcript_exon_variant | Exon 1 of 10 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152266Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.00000429 AC: 1AN: 232894Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 127828
GnomAD4 exome AF: 0.00000413 AC: 6AN: 1452400Hom.: 0 Cov.: 31 AF XY: 0.00000138 AC XY: 1AN XY: 722704
GnomAD4 genome AF: 0.00000656 AC: 1AN: 152384Hom.: 0 Cov.: 33 AF XY: 0.00 AC XY: 0AN XY: 74522
ClinVar
Submissions by phenotype
ALG1-congenital disorder of glycosylation Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at