chr6-145501856-A-G
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The ENST00000450221.6(EPM2A):c.395-9T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.47 in 470,816 control chromosomes in the GnomAD database, including 52,840 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Consequence
ENST00000450221.6 intron
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Benign. Variant got -14 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
EPM2A | ENST00000638717.1 | c.553+666T>C | intron_variant | Intron 4 of 4 | 5 | ENSP00000491330.1 | ||||
EPM2A | ENST00000450221.6 | c.395-9T>C | intron_variant | Intron 3 of 3 | 3 | ENSP00000414900.2 |
Frequencies
GnomAD3 genomes AF: 0.450 AC: 68398AN: 151940Hom.: 15431 Cov.: 32
GnomAD3 exomes AF: 0.470 AC: 70051AN: 148992Hom.: 16848 AF XY: 0.480 AC XY: 38502AN XY: 80256
GnomAD4 exome AF: 0.479 AC: 152807AN: 318758Hom.: 37386 Cov.: 0 AF XY: 0.490 AC XY: 88182AN XY: 180078
GnomAD4 genome AF: 0.450 AC: 68465AN: 152058Hom.: 15454 Cov.: 32 AF XY: 0.456 AC XY: 33870AN XY: 74334
ClinVar
Submissions by phenotype
not specified Benign:1
This variant is classified as Benign based on local population frequency. This variant was detected in 62% of patients studied in a panel designed for Epileptic and Developmental Encephalopathy and Progressive Myoclonus Epilepsy. Number of patients: 58. Only high quality variants are reported. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at