15-39972904-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001013703.4(EIF2AK4):c.1554-4C>T variant causes a splice region, splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000223 in 1,612,552 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 2/2 splice prediction tools predict no significant impact on normal splicing. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Consequence
NM_001013703.4 splice_region, splice_polypyrimidine_tract, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
EIF2AK4 | NM_001013703.4 | c.1554-4C>T | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | ENST00000263791.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
EIF2AK4 | ENST00000263791.10 | c.1554-4C>T | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | 2 | NM_001013703.4 | P1 | |||
EIF2AK4 | ENST00000559624.5 | c.1554-4C>T | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | 1 | |||||
EIF2AK4 | ENST00000560855.5 | c.970-4C>T | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | 5 |
Frequencies
GnomAD3 genomes AF: 0.0000197 AC: 3AN: 151970Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000681 AC: 17AN: 249490Hom.: 0 AF XY: 0.0000665 AC XY: 9AN XY: 135364
GnomAD4 exome AF: 0.0000226 AC: 33AN: 1460582Hom.: 0 Cov.: 30 AF XY: 0.0000289 AC XY: 21AN XY: 726680
GnomAD4 genome AF: 0.0000197 AC: 3AN: 151970Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74202
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at