rs145518377
Variant summary
Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_ModerateBP6BS1BS2
The NM_001099922.3(ALG13):āc.371A>Gā(p.Tyr124Cys) variant causes a missense change. The variant allele was found at a frequency of 0.0000746 in 1,207,228 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 23 hemizygotes in GnomAD. In-silico tool predicts 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. Y124Y) 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 -11 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ALG13 | NM_001099922.3 | c.371A>G | p.Tyr124Cys | missense_variant | 3/27 | ENST00000394780.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ALG13 | ENST00000394780.8 | c.371A>G | p.Tyr124Cys | missense_variant | 3/27 | 2 | NM_001099922.3 | A2 |
Frequencies
GnomAD3 genomes AF: 0.000331 AC: 37AN: 111909Hom.: 0 Cov.: 23 AF XY: 0.000352 AC XY: 12AN XY: 34071
GnomAD3 exomes AF: 0.000174 AC: 31AN: 178246Hom.: 0 AF XY: 0.000111 AC XY: 7AN XY: 63028
GnomAD4 exome AF: 0.0000484 AC: 53AN: 1095266Hom.: 0 Cov.: 29 AF XY: 0.0000305 AC XY: 11AN XY: 360844
GnomAD4 genome AF: 0.000330 AC: 37AN: 111962Hom.: 0 Cov.: 23 AF XY: 0.000352 AC XY: 12AN XY: 34134
ClinVar
Submissions by phenotype
not provided Uncertain:2
Uncertain significance, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | May 01, 2016 | - - |
Uncertain significance, criteria provided, single submitter | clinical testing | GeneDx | Jul 12, 2021 | Has not been previously published as pathogenic or benign to our knowledge; In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; This variant is associated with the following publications: (PMID: 27535533) - |
Developmental and epileptic encephalopathy, 36 Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jan 16, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at