rs13447354
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_004681.4(EIF1AY):c.338-419G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.076 ( 0 hom., 2582 hem., cov: 0)
Exomes 𝑓: 0.072 ( 0 hom. 103 hem. )
Consequence
EIF1AY
NM_004681.4 intron
NM_004681.4 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.222
Genes affected
EIF1AY (HGNC:3252): (eukaryotic translation initiation factor 1A Y-linked) This gene is located on the non-recombining region of the Y chromosome. It encodes a protein related to eukaryotic translation initiation factor 1A (EIF1A), which may function in stabilizing the binding of the initiator Met-tRNA to 40S ribosomal subunits. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jul 2013]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.92).
BA1
?
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.111 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
EIF1AY | NM_004681.4 | c.338-419G>A | intron_variant | ENST00000361365.7 | |||
EIF1AY | NM_001278612.2 | c.287-419G>A | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
EIF1AY | ENST00000361365.7 | c.338-419G>A | intron_variant | 1 | NM_004681.4 | P1 | |||
EIF1AY | ENST00000382772.3 | c.287-419G>A | intron_variant | 1 | |||||
EIF1AY | ENST00000464196.5 | n.2348G>A | non_coding_transcript_exon_variant | 1/2 | 2 | ||||
EIF1AY | ENST00000485584.1 | n.260-419G>A | intron_variant, non_coding_transcript_variant | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.0758 AC: 2584AN: 34070Hom.: 0 Cov.: 0 AF XY: 0.0758 AC XY: 2584AN XY: 34070
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GnomAD4 exome AF: 0.0718 AC: 103AN: 1435Hom.: 0 Cov.: 0 AF XY: 0.0718 AC XY: 103AN XY: 1435
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GnomAD4 genome ? AF: 0.0756 AC: 2582AN: 34132Hom.: 0 Cov.: 0 AF XY: 0.0756 AC XY: 2582AN XY: 34132
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ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
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Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at