NM_004094.5:c.927G>A
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2
The NM_004094.5(EIF2S1):c.927G>A(p.Met309Ile) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0000155 in 1,613,320 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_004094.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
EIF2S1 | ENST00000256383.11 | c.927G>A | p.Met309Ile | missense_variant | Exon 8 of 8 | 1 | NM_004094.5 | ENSP00000256383.4 | ||
EIF2S1 | ENST00000466499.6 | c.927G>A | p.Met309Ile | missense_variant | Exon 7 of 7 | 1 | ENSP00000425299.1 | |||
EIF2S1 | ENST00000554332.1 | n.285G>A | non_coding_transcript_exon_variant | Exon 2 of 2 | 2 |
Frequencies
GnomAD3 genomes AF: 0.0000263 AC: 4AN: 152140Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000477 AC: 12AN: 251334Hom.: 0 AF XY: 0.0000589 AC XY: 8AN XY: 135836
GnomAD4 exome AF: 0.0000144 AC: 21AN: 1461180Hom.: 0 Cov.: 30 AF XY: 0.0000151 AC XY: 11AN XY: 726928
GnomAD4 genome AF: 0.0000263 AC: 4AN: 152140Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74326
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.927G>A (p.M309I) alteration is located in exon 8 (coding exon 7) of the EIF2S1 gene. This alteration results from a G to A substitution at nucleotide position 927, causing the methionine (M) at amino acid position 309 to be replaced by an isoleucine (I). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at