NM_130839.5:c.373T>C
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BA1
This summary comes from the ClinGen Evidence Repository: The allele frequency of the c.313T>C p.(Leu105=) variant in UBE3A (NM_130838.2) is 7.5% in African/African-American sub population in gnomAD, which is high enough to be classified as benign based on thresholds defined by the ClinGen Rett/Angelman-like Expert Panel for Rett/AS-like conditions (BA1). In summary, the c.313T>C p.(Leu105=) variant in UBE3A is classified as Benign based on the ACMG/AMP criteria (BA1). LINK:https://erepo.genome.network/evrepo/ui/classification/CA149410/MONDO:0007113/016
Frequency
Consequence
NM_130839.5 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -8 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0213 AC: 3247AN: 152146Hom.: 120 Cov.: 32
GnomAD3 exomes AF: 0.00561 AC: 1380AN: 245968Hom.: 51 AF XY: 0.00423 AC XY: 565AN XY: 133678
GnomAD4 exome AF: 0.00206 AC: 2999AN: 1456882Hom.: 100 Cov.: 32 AF XY: 0.00174 AC XY: 1265AN XY: 724966
GnomAD4 genome AF: 0.0214 AC: 3251AN: 152264Hom.: 120 Cov.: 32 AF XY: 0.0205 AC XY: 1524AN XY: 74442
ClinVar
Submissions by phenotype
Angelman syndrome Uncertain:1Benign:2
The allele frequency of the c.313T>C p.(Leu105=) variant in UBE3A (NM_130838.2) is 7.5% in African/African-American sub population in gnomAD, which is high enough to be classified as benign based on thresholds defined by the ClinGen Rett/Angelman-like Expert Panel for Rett/AS-like conditions (BA1). In summary, the c.313T>C p.(Leu105=) variant in UBE3A is classified as Benign based on the ACMG/AMP criteria (BA1). -
possible diagnosis of Angelman syndrome -
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not specified Benign:3
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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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. -
not provided Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at