chr16-5071867-G-T
Variant summary
Our verdict is Likely benign. Variant got -3 ACMG points: 2P and 5B. PM2BP4_StrongBP6
The NM_019109.5(ALG1):c.18G>T(p.Leu6Phe) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000237 in 1,604,960 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 16/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars). Synonymous variant affecting the same amino acid position (i.e. L6L) has been classified as Likely benign.
Frequency
Consequence
NM_019109.5 missense
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/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ALG1 | NM_019109.5 | c.18G>T | p.Leu6Phe | missense_variant | 1/13 | ENST00000262374.10 | |
ALG1 | XM_017023457.3 | c.18G>T | p.Leu6Phe | missense_variant | 1/12 | ||
ALG1 | XR_007064892.1 | n.25G>T | non_coding_transcript_exon_variant | 1/10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ALG1 | ENST00000262374.10 | c.18G>T | p.Leu6Phe | missense_variant | 1/13 | 1 | NM_019109.5 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000525 AC: 8AN: 152246Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000907 AC: 21AN: 231474Hom.: 0 AF XY: 0.000110 AC XY: 14AN XY: 126996
GnomAD4 exome AF: 0.0000213 AC: 31AN: 1452598Hom.: 0 Cov.: 31 AF XY: 0.0000263 AC XY: 19AN XY: 722698
GnomAD4 genome ? AF: 0.0000459 AC: 7AN: 152362Hom.: 0 Cov.: 33 AF XY: 0.0000403 AC XY: 3AN XY: 74512
ClinVar
Submissions by phenotype
Inborn genetic diseases Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Feb 06, 2023 | The c.18G>T (p.L6F) alteration is located in exon 1 (coding exon 1) of the ALG1 gene. This alteration results from a G to T substitution at nucleotide position 18, causing the leucine (L) at amino acid position 6 to be replaced by a phenylalanine (F). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
ALG1-congenital disorder of glycosylation Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jan 04, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at