NM_001099922.3:c.2672C>T
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The NM_001099922.3(ALG13):c.2672C>T(p.Ser891Phe) variant causes a missense change. The variant allele was found at a frequency of 0.003 in 1,206,632 control chromosomes in the GnomAD database, including 25 homozygotes. There are 1,256 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Consequence
NM_001099922.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00364 AC: 408AN: 111964Hom.: 1 Cov.: 23 AF XY: 0.00536 AC XY: 183AN XY: 34124
GnomAD3 exomes AF: 0.00512 AC: 888AN: 173528Hom.: 8 AF XY: 0.00525 AC XY: 323AN XY: 61564
GnomAD4 exome AF: 0.00294 AC: 3215AN: 1094616Hom.: 24 Cov.: 29 AF XY: 0.00298 AC XY: 1073AN XY: 360300
GnomAD4 genome AF: 0.00364 AC: 408AN: 112016Hom.: 1 Cov.: 23 AF XY: 0.00535 AC XY: 183AN XY: 34186
ClinVar
Submissions by phenotype
not provided Benign:3
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not specified Benign:2
This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. -
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Developmental and epileptic encephalopathy, 36 Benign:2
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Inborn genetic diseases Benign:1
This alteration is classified as 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