rs45574638
Variant summary
Our verdict is Benign. Variant got -18 ACMG points: 0P and 18B. BP4_ModerateBP6_Very_StrongBS1BS2
The NM_024740.2(ALG9):c.406-7C>T variant causes a splice region, splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0319 in 1,548,022 control chromosomes in the GnomAD database, including 906 homozygotes. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Benign (★★).
Frequency
Consequence
NM_024740.2 splice_region, splice_polypyrimidine_tract, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -18 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ALG9 | NM_024740.2 | c.406-7C>T | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | ENST00000616540.5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ALG9 | ENST00000616540.5 | c.406-7C>T | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | 1 | NM_024740.2 |
Frequencies
GnomAD3 genomes ? AF: 0.0252 AC: 3830AN: 152034Hom.: 78 Cov.: 33
GnomAD3 exomes AF: 0.0251 AC: 3942AN: 157232Hom.: 59 AF XY: 0.0253 AC XY: 2095AN XY: 82680
GnomAD4 exome AF: 0.0326 AC: 45528AN: 1395870Hom.: 828 Cov.: 29 AF XY: 0.0319 AC XY: 21974AN XY: 688562
GnomAD4 genome ? AF: 0.0252 AC: 3831AN: 152152Hom.: 78 Cov.: 33 AF XY: 0.0255 AC XY: 1894AN XY: 74394
ClinVar
Submissions by phenotype
not specified Benign:2
Benign, criteria provided, single submitter | clinical testing | Eurofins Ntd Llc (ga) | May 29, 2013 | - - |
Benign, criteria provided, single submitter | clinical testing | GeneDx | Jan 25, 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. - |
ALG9 congenital disorder of glycosylation Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 26, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at