rs17851770
Variant summary
Our verdict is Benign. Variant got -18 ACMG points: 2P and 20B. PM5BP4_StrongBP6_Very_StrongBA1
The NM_018100.4(EFHC1):āc.1855A>Cā(p.Ile619Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.082 in 1,613,132 control chromosomes in the GnomAD database, including 6,446 homozygotes. In-silico tool predicts a benign outcome for this variant. 12/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (ā ā ). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. I619S) has been classified as Likely benign.
Frequency
Consequence
NM_018100.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -18 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
EFHC1 | NM_018100.4 | c.1855A>C | p.Ile619Leu | missense_variant | 11/11 | ENST00000371068.11 | |
EFHC1 | NM_001172420.2 | c.1798A>C | p.Ile600Leu | missense_variant | 12/12 | ||
EFHC1 | NR_033327.2 | n.3181A>C | non_coding_transcript_exon_variant | 10/10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
EFHC1 | ENST00000371068.11 | c.1855A>C | p.Ile619Leu | missense_variant | 11/11 | 1 | NM_018100.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0611 AC: 9294AN: 152128Hom.: 448 Cov.: 32
GnomAD3 exomes AF: 0.0619 AC: 15553AN: 251068Hom.: 701 AF XY: 0.0621 AC XY: 8433AN XY: 135742
GnomAD4 exome AF: 0.0842 AC: 122982AN: 1460886Hom.: 5999 Cov.: 32 AF XY: 0.0820 AC XY: 59623AN XY: 726758
GnomAD4 genome ? AF: 0.0610 AC: 9290AN: 152246Hom.: 447 Cov.: 32 AF XY: 0.0602 AC XY: 4480AN XY: 74438
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 | - | - - |
Juvenile myoclonic epilepsy Benign:2
Likely benign, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Jun 14, 2016 | - - |
Benign, criteria provided, single submitter | clinical testing | Athena Diagnostics | Apr 28, 2017 | - - |
Absence seizure;C1850778:Myoclonic epilepsy, juvenile, susceptibility to, 1 Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 24, 2024 | - - |
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