rs772766102
Variant summary
Our verdict is Benign. Variant got -15 ACMG points: 1P and 16B. PM4_SupportingBP6_Very_StrongBS1BS2
The NM_001099922.3(ALG13):c.2383_2385delGAA(p.Glu795del) variant causes a conservative inframe deletion change. The variant allele was found at a frequency of 0.000907 in 1,208,532 control chromosomes in the GnomAD database, including 1 homozygotes. There are 330 hemizygotes in GnomAD. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Consequence
NM_001099922.3 conservative_inframe_deletion
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -15 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.000604 AC: 68AN: 112490Hom.: 0 Cov.: 23 AF XY: 0.000519 AC XY: 18AN XY: 34654
GnomAD3 exomes AF: 0.000439 AC: 78AN: 177526Hom.: 0 AF XY: 0.000366 AC XY: 24AN XY: 65508
GnomAD4 exome AF: 0.000938 AC: 1028AN: 1096042Hom.: 1 AF XY: 0.000863 AC XY: 312AN XY: 361688
GnomAD4 genome AF: 0.000604 AC: 68AN: 112490Hom.: 0 Cov.: 23 AF XY: 0.000519 AC XY: 18AN XY: 34654
ClinVar
Submissions by phenotype
not provided Benign:7
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See Variant Classification Assertion Criteria. -
ALG13: BS2 -
Developmental and epileptic encephalopathy, 36 Benign:2
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Inborn genetic diseases Benign:1
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. -
ALG13-related disorder Benign:1
This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at