14-75003054-C-T
Variant summary
Our verdict is Benign. Variant got -7 ACMG points: 2P and 9B. PM2BP4_ModerateBP6_ModerateBP7BS1
The NM_014239.4(EIF2B2):c.64C>T(p.Leu22=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000125 in 1,614,112 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 Benign (★). Synonymous variant affecting the same amino acid position (i.e. L22L) has been classified as Likely benign.
Frequency
Consequence
NM_014239.4 synonymous
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 |
---|---|---|---|---|---|---|---|
EIF2B2 | NM_014239.4 | c.64C>T | p.Leu22= | synonymous_variant | 1/8 | ENST00000266126.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
EIF2B2 | ENST00000266126.10 | c.64C>T | p.Leu22= | synonymous_variant | 1/8 | 1 | NM_014239.4 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000986 AC: 15AN: 152172Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.000334 AC: 84AN: 251132Hom.: 0 AF XY: 0.000405 AC XY: 55AN XY: 135852
GnomAD4 exome AF: 0.000127 AC: 186AN: 1461822Hom.: 0 Cov.: 33 AF XY: 0.000127 AC XY: 92AN XY: 727214
GnomAD4 genome AF: 0.0000985 AC: 15AN: 152290Hom.: 0 Cov.: 31 AF XY: 0.000107 AC XY: 8AN XY: 74458
ClinVar
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 29, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at