chr16-5071857-C-A
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The NM_019109.5(ALG1):c.8C>A(p.Ala3Asp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000403 in 1,604,626 control chromosomes in the GnomAD database, including 12 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. A3T) has been classified as Uncertain significance.
Frequency
Consequence
NM_019109.5 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 rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
ALG1 | NM_019109.5 | c.8C>A | p.Ala3Asp | missense_variant | Exon 1 of 13 | ENST00000262374.10 | NP_061982.3 | |
ALG1 | XM_017023457.3 | c.8C>A | p.Ala3Asp | missense_variant | Exon 1 of 12 | XP_016878946.1 | ||
ALG1 | XR_007064892.1 | n.15C>A | non_coding_transcript_exon_variant | Exon 1 of 10 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.000223 AC: 34AN: 152250Hom.: 1 Cov.: 33
GnomAD3 exomes AF: 0.000958 AC: 223AN: 232826Hom.: 3 AF XY: 0.00127 AC XY: 162AN XY: 127816
GnomAD4 exome AF: 0.000421 AC: 611AN: 1452260Hom.: 11 Cov.: 31 AF XY: 0.000606 AC XY: 438AN XY: 722670
GnomAD4 genome AF: 0.000230 AC: 35AN: 152366Hom.: 1 Cov.: 33 AF XY: 0.000389 AC XY: 29AN XY: 74514
ClinVar
Submissions by phenotype
ALG1-congenital disorder of glycosylation Benign:2
- -
- -
not provided Benign:1
ALG1: BS2 -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at