7-74195293-A-G
Variant names:
Variant summary
Our verdict is Benign. The variant received -11 ACMG points: 0P and 11B. BP4_StrongBP6_ModerateBP7BS2
The NM_022170.2(EIF4H):c.732A>G(p.Gln244Gln) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000434 in 1,613,748 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 Likely benign (★).
Frequency
Genomes: 𝑓 0.0000066 ( 0 hom., cov: 32)
Exomes 𝑓: 0.0000041 ( 0 hom. )
Consequence
EIF4H
NM_022170.2 synonymous
NM_022170.2 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.0740
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 was made for transcript
Our verdict: Benign. The variant received -11 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.89).
BP6
Variant 7-74195293-A-G is Benign according to our data. Variant chr7-74195293-A-G is described in ClinVar as [Likely_benign]. Clinvar id is 2657585.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
Synonymous conserved (PhyloP=-0.074 with no splicing effect.
BS2
High AC in GnomAdExome4 at 6 AD gene.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152168Hom.: 0 Cov.: 32 show subpopulations
GnomAD3 genomes
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1
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152168
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32
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GnomAD2 exomes AF: 0.00000797 AC: 2AN: 250940 AF XY: 0.00000737 show subpopulations
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2
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250940
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GnomAD4 exome AF: 0.00000411 AC: 6AN: 1461580Hom.: 0 Cov.: 31 AF XY: 0.00000825 AC XY: 6AN XY: 727108 show subpopulations
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6
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1461580
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31
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727108
Gnomad4 AFR exome
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1
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33468
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44714
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26132
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0
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39700
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86240
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1
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53418
Gnomad4 NFE exome
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4
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1111814
Gnomad4 Remaining exome
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0
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60370
Heterozygous variant carriers
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GnomAD4 genome AF: 0.00000657 AC: 1AN: 152168Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74322 show subpopulations
GnomAD4 genome
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AC:
1
AN:
152168
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32
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0
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74322
Gnomad4 AFR
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0.0000241313
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0.0000241313
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Genome Het
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Aug 01, 2022
CeGaT Center for Human Genetics Tuebingen
Significance:Likely benign
Review Status:criteria provided, single submitter
Collection Method:clinical testing
EIF4H: BP4, BP7 -
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
DANN
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
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