chrX-24057745-A-G
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 1P and 13B. PP2BP4_StrongBP6BA1
The NM_001415.4(EIF2S3):āc.374A>Gā(p.Lys125Arg) variant causes a missense change. The variant allele was found at a frequency of 0.148 in 1,205,280 control chromosomes in the GnomAD database, including 9,523 homozygotes. There are 60,594 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (no stars). Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.
Frequency
Consequence
NM_001415.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -12 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
EIF2S3 | NM_001415.4 | c.374A>G | p.Lys125Arg | missense_variant | 4/12 | ENST00000253039.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
EIF2S3 | ENST00000253039.9 | c.374A>G | p.Lys125Arg | missense_variant | 4/12 | 1 | NM_001415.4 | P1 | |
EIF2S3 | ENST00000423068.1 | c.374A>G | p.Lys125Arg | missense_variant | 4/5 | 2 | |||
EIF2S3 | ENST00000487075.1 | n.156+2067A>G | intron_variant, non_coding_transcript_variant | 5 |
Frequencies
GnomAD3 genomes AF: 0.117 AC: 13120AN: 111859Hom.: 701 Cov.: 24 AF XY: 0.113 AC XY: 3862AN XY: 34027
GnomAD3 exomes AF: 0.146 AC: 25860AN: 177160Hom.: 1347 AF XY: 0.156 AC XY: 9788AN XY: 62562
GnomAD4 exome AF: 0.151 AC: 165458AN: 1093368Hom.: 8820 Cov.: 30 AF XY: 0.158 AC XY: 56726AN XY: 359640
GnomAD4 genome AF: 0.117 AC: 13127AN: 111912Hom.: 703 Cov.: 24 AF XY: 0.113 AC XY: 3868AN XY: 34090
ClinVar
Submissions by phenotype
not specified Benign:1
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. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at