chr17-44852291-G-C
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_004247.4(EFTUD2):c.2715+118C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0726 in 1,286,060 control chromosomes in the GnomAD database, including 3,966 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.055 ( 290 hom., cov: 31)
Exomes 𝑓: 0.075 ( 3676 hom. )
Consequence
EFTUD2
NM_004247.4 intron
NM_004247.4 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: 1.12
Genes affected
EFTUD2 (HGNC:30858): (elongation factor Tu GTP binding domain containing 2) This gene encodes a GTPase which is a component of the spliceosome complex which processes precursor mRNAs to produce mature mRNAs. Mutations in this gene are associated with mandibulofacial dysostosis with microcephaly. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Apr 2012]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -14 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.84).
BP6
?
Variant 17-44852291-G-C is Benign according to our data. Variant chr17-44852291-G-C is described in ClinVar as [Benign]. Clinvar id is 1263536.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
?
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0774 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
EFTUD2 | NM_004247.4 | c.2715+118C>G | intron_variant | ENST00000426333.7 | |||
EFTUD2 | NM_001142605.2 | c.2610+118C>G | intron_variant | ||||
EFTUD2 | NM_001258353.2 | c.2715+118C>G | intron_variant | ||||
EFTUD2 | NM_001258354.2 | c.2685+118C>G | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
EFTUD2 | ENST00000426333.7 | c.2715+118C>G | intron_variant | 1 | NM_004247.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0549 AC: 8332AN: 151664Hom.: 289 Cov.: 31
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GnomAD4 exome AF: 0.0750 AC: 85024AN: 1134278Hom.: 3676 AF XY: 0.0729 AC XY: 41077AN XY: 563094
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GnomAD4 genome ? AF: 0.0550 AC: 8345AN: 151782Hom.: 290 Cov.: 31 AF XY: 0.0514 AC XY: 3810AN XY: 74176
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | Jul 09, 2018 | - - |
Computational scores
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Name
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BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at