rs776140816
Variant summary
Our verdict is Likely pathogenic. Variant got 8 ACMG points: 8P and 0B. PVS1_ModeratePM2PP3_Strong
The NM_001013703.4(EIF2AK4):c.4065+1G>A variant causes a splice donor change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.000000686 in 1,457,706 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. 3/3 splice prediction tools predicting alterations to normal splicing. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Consequence
NM_001013703.4 splice_donor
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_pathogenic. Variant got 8 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
EIF2AK4 | NM_001013703.4 | c.4065+1G>A | splice_donor_variant | ENST00000263791.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
EIF2AK4 | ENST00000263791.10 | c.4065+1G>A | splice_donor_variant | 2 | NM_001013703.4 | P1 | |||
EIF2AK4 | ENST00000558629.5 | n.2982+1G>A | splice_donor_variant, non_coding_transcript_variant | 1 | |||||
EIF2AK4 | ENST00000560855.5 | c.3397+1G>A | splice_donor_variant | 5 | |||||
EIF2AK4 | ENST00000558557.1 | n.1057+1G>A | splice_donor_variant, non_coding_transcript_variant | 2 |
Frequencies
GnomAD3 genomes Cov.: 31
GnomAD3 exomes AF: 0.00000401 AC: 1AN: 249176Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 135172
GnomAD4 exome AF: 6.86e-7 AC: 1AN: 1457706Hom.: 0 Cov.: 30 AF XY: 0.00 AC XY: 0AN XY: 724572
GnomAD4 genome Cov.: 31
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at