6-52454128-G-T
Variant summary
Our verdict is Uncertain significance. Variant got 4 ACMG points: 4P and 0B. PM2PP3_Moderate
The NM_018100.4(EFHC1):c.757G>T(p.Asp253Tyr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000274 in 1,461,688 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as risk factor (no stars). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. D253N) has been classified as Uncertain significance.
Frequency
Consequence
NM_018100.4 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Uncertain_significance. Variant got 4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
EFHC1 | NM_018100.4 | c.757G>T | p.Asp253Tyr | missense_variant | 5/11 | ENST00000371068.11 | |
EFHC1 | NM_001172420.2 | c.700G>T | p.Asp234Tyr | missense_variant | 6/12 | ||
EFHC1 | NR_033327.2 | n.2083G>T | non_coding_transcript_exon_variant | 4/10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
EFHC1 | ENST00000371068.11 | c.757G>T | p.Asp253Tyr | missense_variant | 5/11 | 1 | NM_018100.4 | P1 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 exomes AF: 0.0000199 AC: 5AN: 251398Hom.: 0 AF XY: 0.0000221 AC XY: 3AN XY: 135864
GnomAD4 exome AF: 0.00000274 AC: 4AN: 1461688Hom.: 0 Cov.: 34 AF XY: 0.00000413 AC XY: 3AN XY: 727144
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
Myoclonic epilepsy, juvenile, susceptibility to, 1 Other:1
risk factor, no assertion criteria provided | literature only | OMIM | Aug 01, 2004 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at