rs766772102
Variant summary
Our verdict is Benign. Variant got -18 ACMG points: 0P and 18B. BP4_ModerateBP6_Very_StrongBS1BS2
The NM_001099922.3(ALG13):āc.1922A>Gā(p.His641Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000198 in 1,209,507 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 7 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. 11/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (ā ā ). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. H641D) has been classified as Likely benign.
Frequency
Consequence
NM_001099922.3 missense
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 |
---|---|---|---|---|---|---|---|
ALG13 | NM_001099922.3 | c.1922A>G | p.His641Arg | missense_variant | 16/27 | ENST00000394780.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ALG13 | ENST00000394780.8 | c.1922A>G | p.His641Arg | missense_variant | 16/27 | 2 | NM_001099922.3 | A2 |
Frequencies
GnomAD3 genomes ? AF: 0.00000896 AC: 1AN: 111636Hom.: 0 Cov.: 23 AF XY: 0.00 AC XY: 0AN XY: 33820
GnomAD3 exomes AF: 0.000101 AC: 18AN: 179073Hom.: 0 AF XY: 0.0000897 AC XY: 6AN XY: 66873
GnomAD4 exome AF: 0.0000209 AC: 23AN: 1097871Hom.: 0 Cov.: 30 AF XY: 0.0000193 AC XY: 7AN XY: 363315
GnomAD4 genome ? AF: 0.00000896 AC: 1AN: 111636Hom.: 0 Cov.: 23 AF XY: 0.00 AC XY: 0AN XY: 33820
ClinVar
Submissions by phenotype
Developmental and epileptic encephalopathy, 36 Benign:2
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Dec 27, 2023 | - - |
Likely benign, criteria provided, single submitter | clinical testing | Fulgent Genetics, Fulgent Genetics | Jan 24, 2022 | - - |
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Jan 13, 2020 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at