rs17146094
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_022170.2(EIF4H):c.607+107A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0275 in 1,507,180 control chromosomes in the GnomAD database, including 1,179 homozygotes. 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 0.031 ( 175 hom., cov: 32)
Exomes 𝑓: 0.027 ( 1004 hom. )
Consequence
EIF4H
NM_022170.2 intron
NM_022170.2 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.431
Genes affected
EIF4H (HGNC:12741): (eukaryotic translation initiation factor 4H) This gene encodes one of the translation initiation factors, which functions to stimulate the initiation of protein synthesis at the level of mRNA utilization. This gene is deleted in Williams syndrome, a multisystem developmental disorder caused by the deletion of contiguous genes at 7q11.23. Alternative splicing of this gene generates 2 transcript variants. [provided by RefSeq, Jul 2008]
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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=-0.86).
BA1
?
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.15 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
EIF4H | NM_022170.2 | c.607+107A>G | intron_variant | ENST00000265753.13 | |||
EIF4H | NM_031992.2 | c.547+107A>G | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
EIF4H | ENST00000265753.13 | c.607+107A>G | intron_variant | 2 | NM_022170.2 |
Frequencies
GnomAD3 genomes ? AF: 0.0313 AC: 4765AN: 152226Hom.: 169 Cov.: 32
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GnomAD4 exome AF: 0.0270 AC: 36648AN: 1354836Hom.: 1004 Cov.: 28 AF XY: 0.0272 AC XY: 18031AN XY: 662172
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GnomAD4 genome ? AF: 0.0314 AC: 4781AN: 152344Hom.: 175 Cov.: 32 AF XY: 0.0354 AC XY: 2637AN XY: 74494
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3478
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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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at