6-145686196-C-T
Variant summary
Our verdict is Benign. Variant got -19 ACMG points: 0P and 19B. BP4_ModerateBP6_Very_StrongBP7BA1
The NM_005670.4(EPM2A):c.402G>A(p.Gly134Gly) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.226 in 1,612,596 control chromosomes in the GnomAD database, including 44,761 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Consequence
NM_005670.4 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -19 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.183 AC: 27793AN: 151958Hom.: 3304 Cov.: 32
GnomAD3 exomes AF: 0.214 AC: 53770AN: 251320Hom.: 7079 AF XY: 0.210 AC XY: 28476AN XY: 135826
GnomAD4 exome AF: 0.230 AC: 335864AN: 1460518Hom.: 41458 Cov.: 33 AF XY: 0.228 AC XY: 165746AN XY: 726626
GnomAD4 genome AF: 0.183 AC: 27795AN: 152078Hom.: 3303 Cov.: 32 AF XY: 0.180 AC XY: 13395AN XY: 74336
ClinVar
Submissions by phenotype
not specified Benign:3
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Likely benign based on allele frequency in 1000 Genomes Project or ESP global frequency and its presence in a patient with a rare or unrelated disease phenotype. NOT Sanger confirmed. -
This variant is classified as Benign based on local population frequency. This variant was detected in 55% of patients studied in a panel designed for Epileptic and Developmental Encephalopathy and Progressive Myoclonus Epilepsy. Number of patients: 51. Only high quality variants are reported. -
not provided Benign:2
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Lafora disease Benign:1
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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. -
Progressive myoclonic epilepsy Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at