14-67380676-A-G
Variant summary
Our verdict is Likely benign. Variant got -3 ACMG points: 1P and 4B. PP3BS2
The NM_004094.5(EIF2S1):āc.491A>Gā(p.Asp164Gly) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.000029 in 1,413,934 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 Uncertain significance (ā ).
Frequency
Consequence
NM_004094.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -3 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
EIF2S1 | ENST00000256383.11 | c.491A>G | p.Asp164Gly | missense_variant | Exon 5 of 8 | 1 | NM_004094.5 | ENSP00000256383.4 | ||
EIF2S1 | ENST00000466499.6 | c.491A>G | p.Asp164Gly | missense_variant | Exon 4 of 7 | 1 | ENSP00000425299.1 | |||
EIF2S1 | ENST00000557310.5 | c.491A>G | p.Asp164Gly | missense_variant | Exon 5 of 7 | 2 | ENSP00000451975.1 | |||
EIF2S1 | ENST00000555876.1 | c.359A>G | p.Asp120Gly | missense_variant | Exon 4 of 6 | 2 | ENSP00000452034.1 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 exomes AF: 0.0000136 AC: 3AN: 219928Hom.: 0 AF XY: 0.00000832 AC XY: 1AN XY: 120212
GnomAD4 exome AF: 0.0000290 AC: 41AN: 1413934Hom.: 0 Cov.: 28 AF XY: 0.0000313 AC XY: 22AN XY: 703020
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.491A>G (p.D164G) alteration is located in exon 5 (coding exon 4) of the EIF2S1 gene. This alteration results from a A to G substitution at nucleotide position 491, causing the aspartic acid (D) at amino acid position 164 to be replaced by a glycine (G). 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