chrX-111711720-C-T
Variant summary
Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP6BS1BS2
The NM_001099922.3(ALG13):c.880C>T(p.Pro294Ser) variant causes a missense change. The variant allele was found at a frequency of 0.0000723 in 1,202,997 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 32 hemizygotes in GnomAD. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. P294A) 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 -9 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ALG13 | NM_001099922.3 | c.880C>T | p.Pro294Ser | missense_variant | 6/27 | ENST00000394780.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ALG13 | ENST00000394780.8 | c.880C>T | p.Pro294Ser | missense_variant | 6/27 | 2 | NM_001099922.3 | A2 |
Frequencies
GnomAD3 genomes AF: 0.0000268 AC: 3AN: 111866Hom.: 0 Cov.: 23 AF XY: 0.0000586 AC XY: 2AN XY: 34102
GnomAD3 exomes AF: 0.0000635 AC: 11AN: 173246Hom.: 0 AF XY: 0.0000976 AC XY: 6AN XY: 61488
GnomAD4 exome AF: 0.0000770 AC: 84AN: 1091078Hom.: 0 Cov.: 28 AF XY: 0.0000840 AC XY: 30AN XY: 357022
GnomAD4 genome AF: 0.0000268 AC: 3AN: 111919Hom.: 0 Cov.: 23 AF XY: 0.0000585 AC XY: 2AN XY: 34165
ClinVar
Submissions by phenotype
Developmental and epileptic encephalopathy, 1 Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Genomic Research Center, Shahid Beheshti University of Medical Sciences | Aug 07, 2018 | - - |
Developmental and epileptic encephalopathy, 36 Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 29, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at