chr12-53040179-G-C
Variant summary
Our verdict is Benign. Variant got -7 ACMG points: 1P and 8B. PP2BP4_StrongBS2
The NM_001417.7(EIF4B):c.1792G>C(p.Val598Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000142 in 1,614,048 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001417.7 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -7 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
EIF4B | NM_001417.7 | c.1792G>C | p.Val598Leu | missense_variant | 15/15 | ENST00000262056.14 | |
EIF4B | NM_001300821.3 | c.1807G>C | p.Val603Leu | missense_variant | 15/15 | ||
EIF4B | NM_001330654.2 | c.1675G>C | p.Val559Leu | missense_variant | 14/14 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
EIF4B | ENST00000262056.14 | c.1792G>C | p.Val598Leu | missense_variant | 15/15 | 1 | NM_001417.7 | P4 | |
TNS2-AS1 | ENST00000552905.6 | n.320+5782C>G | intron_variant, non_coding_transcript_variant | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.00000657 AC: 1AN: 152192Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000521 AC: 13AN: 249518Hom.: 0 AF XY: 0.0000739 AC XY: 10AN XY: 135380
GnomAD4 exome AF: 0.0000150 AC: 22AN: 1461856Hom.: 0 Cov.: 31 AF XY: 0.0000151 AC XY: 11AN XY: 727228
GnomAD4 genome ? AF: 0.00000657 AC: 1AN: 152192Hom.: 0 Cov.: 33 AF XY: 0.0000135 AC XY: 1AN XY: 74342
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | May 17, 2023 | The c.1792G>C (p.V598L) alteration is located in exon 15 (coding exon 15) of the EIF4B gene. This alteration results from a G to C substitution at nucleotide position 1792, causing the valine (V) at amino acid position 598 to be replaced by a leucine (L). 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