chrX-24057651-C-A
Variant summary
Our verdict is Uncertain significance. Variant got 3 ACMG points: 3P and 0B. PM2PP2
The NM_001415.4(EIF2S3):c.280C>A(p.Pro94Thr) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.000000911 in 1,097,461 control chromosomes in the GnomAD database, with no homozygous occurrence. There are no hemizygote samples in GnomAD. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. P94R) has been classified as Uncertain significance.
Frequency
Consequence
NM_001415.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 3 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
EIF2S3 | NM_001415.4 | c.280C>A | p.Pro94Thr | missense_variant | 4/12 | ENST00000253039.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
EIF2S3 | ENST00000253039.9 | c.280C>A | p.Pro94Thr | missense_variant | 4/12 | 1 | NM_001415.4 | P1 | |
EIF2S3 | ENST00000423068.1 | c.280C>A | p.Pro94Thr | missense_variant | 4/5 | 2 | |||
EIF2S3 | ENST00000487075.1 | n.156+1973C>A | intron_variant, non_coding_transcript_variant | 5 |
Frequencies
GnomAD3 genomes ? Cov.: 24
GnomAD3 exomes AF: 0.00000550 AC: 1AN: 181950Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 66690
GnomAD4 exome AF: 9.11e-7 AC: 1AN: 1097461Hom.: 0 Cov.: 30 AF XY: 0.00 AC XY: 0AN XY: 362893
GnomAD4 genome ? Cov.: 24
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Genetic Services Laboratory, University of Chicago | Jul 06, 2017 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at