rs3804505
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_018100.4(EFHC1):c.545G>A(p.Arg182His) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0591 in 1,613,812 control chromosomes in the GnomAD database, including 3,170 homozygotes. In-silico tool predicts a benign outcome for this variant. 15/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Consequence
NM_018100.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
EFHC1 | NM_018100.4 | c.545G>A | p.Arg182His | missense_variant | Exon 3 of 11 | ENST00000371068.11 | NP_060570.2 | |
EFHC1 | NM_001172420.2 | c.488G>A | p.Arg163His | missense_variant | Exon 4 of 12 | NP_001165891.1 | ||
EFHC1 | NR_033327.2 | n.614G>A | non_coding_transcript_exon_variant | Exon 3 of 10 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0475 AC: 7224AN: 152040Hom.: 235 Cov.: 32
GnomAD3 exomes AF: 0.0603 AC: 15135AN: 251004Hom.: 552 AF XY: 0.0615 AC XY: 8348AN XY: 135672
GnomAD4 exome AF: 0.0602 AC: 88055AN: 1461652Hom.: 2930 Cov.: 33 AF XY: 0.0602 AC XY: 43806AN XY: 727146
GnomAD4 genome AF: 0.0476 AC: 7241AN: 152160Hom.: 240 Cov.: 32 AF XY: 0.0489 AC XY: 3636AN XY: 74374
ClinVar
Submissions by phenotype
not specified Benign:2
Likely benign, no assertion criteria provided | clinical testing | Genetic Services Laboratory, University of Chicago | - | 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. - |
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | - | - - |
Myoclonic epilepsy, juvenile, susceptibility to, 1 Uncertain:1
Uncertain significance, no assertion criteria provided | literature only | OMIM | Aug 01, 2004 | - - |
Juvenile myoclonic epilepsy Benign:1
Benign, criteria provided, single submitter | clinical testing | Athena Diagnostics | May 08, 2017 | - - |
Absence seizure;C1850778:Myoclonic epilepsy, juvenile, susceptibility to, 1 Benign:1
Benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Jan 22, 2025 | - - |
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | Mar 03, 2015 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at