rs138712375
Variant summary
Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP6BS1BS2
The NM_001099922.3(ALG13):c.2606C>T(p.Ala869Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000794 in 1,208,308 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 32 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. 11/18 in silico tools predict a benign outcome for this variant. 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. A869T) has been classified as Likely benign.
Frequency
Consequence
NM_001099922.3 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Benign. Variant got -13 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ALG13 | NM_001099922.3 | c.2606C>T | p.Ala869Val | missense_variant | 23/27 | ENST00000394780.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ALG13 | ENST00000394780.8 | c.2606C>T | p.Ala869Val | missense_variant | 23/27 | 2 | NM_001099922.3 | A2 |
Frequencies
GnomAD3 genomes AF: 0.000125 AC: 14AN: 111575Hom.: 0 Cov.: 23 AF XY: 0.000119 AC XY: 4AN XY: 33745
GnomAD3 exomes AF: 0.0000560 AC: 10AN: 178483Hom.: 0 AF XY: 0.000106 AC XY: 7AN XY: 66277
GnomAD4 exome AF: 0.0000739 AC: 81AN: 1096677Hom.: 0 Cov.: 29 AF XY: 0.0000773 AC XY: 28AN XY: 362201
GnomAD4 genome AF: 0.000134 AC: 15AN: 111631Hom.: 0 Cov.: 23 AF XY: 0.000118 AC XY: 4AN XY: 33811
ClinVar
Submissions by phenotype
not provided Uncertain:1Benign:2
Uncertain significance, criteria provided, single submitter | clinical testing | Athena Diagnostics | Mar 02, 2018 | - - |
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Jul 01, 2024 | ALG13: BP4, BS2 - |
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Aug 14, 2018 | - - |
Developmental and epileptic encephalopathy, 36 Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Dec 02, 2023 | - - |
Inborn genetic diseases Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Nov 23, 2018 | This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at