rs17113312
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The NM_024740.2(ALG9):c.764C>T(p.Ser255Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00213 in 1,613,976 control chromosomes in the GnomAD database, including 84 homozygotes. 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. S255S) has been classified as Likely benign.
Frequency
Consequence
NM_024740.2 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/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ALG9 | NM_024740.2 | c.764C>T | p.Ser255Leu | missense_variant | 7/15 | ENST00000616540.5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ALG9 | ENST00000616540.5 | c.764C>T | p.Ser255Leu | missense_variant | 7/15 | 1 | NM_024740.2 |
Frequencies
GnomAD3 genomes AF: 0.0113 AC: 1714AN: 152072Hom.: 46 Cov.: 32
GnomAD3 exomes AF: 0.00274 AC: 683AN: 249278Hom.: 10 AF XY: 0.00210 AC XY: 284AN XY: 135248
GnomAD4 exome AF: 0.00118 AC: 1719AN: 1461786Hom.: 37 Cov.: 31 AF XY: 0.00100 AC XY: 729AN XY: 727194
GnomAD4 genome AF: 0.0113 AC: 1718AN: 152190Hom.: 47 Cov.: 32 AF XY: 0.0110 AC XY: 817AN XY: 74402
ClinVar
Submissions by phenotype
not specified Benign:2
Benign, criteria provided, single submitter | clinical testing | Eurofins Ntd Llc (ga) | Nov 28, 2012 | - - |
Benign, criteria provided, single submitter | clinical testing | GeneDx | Apr 06, 2016 | 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. - |
not provided Benign:2
Likely benign, criteria provided, single submitter | clinical testing | Center for Pediatric Genomic Medicine, Children's Mercy Hospital and Clinics | Aug 19, 2015 | - - |
Benign, criteria provided, single submitter | clinical testing | Athena Diagnostics | Mar 02, 2018 | - - |
Gillessen-Kaesbach-Nishimura syndrome;C2931006:ALG9 congenital disorder of glycosylation Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Fulgent Genetics, Fulgent Genetics | Oct 12, 2021 | - - |
ALG9 congenital disorder of glycosylation Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 24, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at