rs531330673
Variant summary
Our verdict is Benign. Variant got -19 ACMG points: 0P and 19B. BP4_ModerateBP6_Very_StrongBP7BS1BS2
The NM_005670.4(EPM2A):c.171G>T(p.Pro57=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000378 in 1,304,038 control chromosomes in the GnomAD database, including 4 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★). Synonymous variant affecting the same amino acid position (i.e. P57P) has been classified as Likely 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
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
EPM2A | NM_005670.4 | c.171G>T | p.Pro57= | synonymous_variant | 1/4 | ENST00000367519.9 | |
EPM2A-DT | NR_038246.1 | n.52+408C>A | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
EPM2A | ENST00000367519.9 | c.171G>T | p.Pro57= | synonymous_variant | 1/4 | 1 | NM_005670.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.000447 AC: 66AN: 147686Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000689 AC: 57AN: 82722Hom.: 1 AF XY: 0.000615 AC XY: 29AN XY: 47128
GnomAD4 exome AF: 0.000369 AC: 427AN: 1156226Hom.: 4 Cov.: 30 AF XY: 0.000357 AC XY: 203AN XY: 568576
GnomAD4 genome ? AF: 0.000447 AC: 66AN: 147812Hom.: 0 Cov.: 32 AF XY: 0.000582 AC XY: 42AN XY: 72134
ClinVar
Submissions by phenotype
not specified Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | Apr 17, 2014 | 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. - |
Inborn genetic diseases Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Aug 08, 2018 | 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. - |
Progressive myoclonic epilepsy Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jan 29, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at