X-24055033-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The NM_001415.4(EIF2S3):c.65C>T(p.Thr22Ile) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. 11/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (no stars). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. T22A) 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 1 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
EIF2S3 | ENST00000253039.9 | c.65C>T | p.Thr22Ile | missense_variant | Exon 1 of 12 | 1 | NM_001415.4 | ENSP00000253039.4 | ||
EIF2S3 | ENST00000423068.1 | c.62C>T | p.Thr21Ile | missense_variant | Exon 1 of 5 | 2 | ENSP00000391383.1 | |||
EIF2S3 | ENST00000487075.1 | n.88C>T | non_coding_transcript_exon_variant | Exon 1 of 3 | 5 |
Frequencies
GnomAD3 genomes Cov.: 23
GnomAD4 exome Cov.: 30
GnomAD4 genome Cov.: 23
ClinVar
Submissions by phenotype
MEHMO syndrome Uncertain:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at